Microsatellite Loci BED File

Question

Microsatellite Loci BED File

Closed this issue 5 years ago · 11 comments

Hello. I have a human tumor bam and normal bam files. I would like to perform MSI test.
I am new to this and I am not sure how to go about making Microsatellite Loci BED File.
Could anyone kindly let me know how I can make one or share with me?
Thanks.

Answer 1 · 2018-09-27T15:19:50.000Z

You can create a BED file with RepeatFinder (provided with MANTIS) and bedtools. To run RepeatFinder:
./RepeatFinder -i /path/to/genome.fasta -o /path/to/all_loci.bed

This will identify putative microsatellite loci throughout the provided genome. Next, this will need to be filtered by your sequencing target region:
bedtools intersect -a /path/to/all_loci.bed -b /path/to/target.bed -wa > /path/to/loci_in_targed.bed

Please let me know if you have any further questions.

Answer 2 · 2018-10-01T13:47:55.000Z

Thank you so much. I was able to make the loci_in_targed.bed.
Now I will try to run the MANTIS.

Answer 3 · 2019-03-28T00:48:20.000Z

I am also new to this. Where can I find the genome.fasta files for grch38 and all_loci.bed file?

Answer 4 · 2019-03-28T16:15:48.000Z

Hello @audyavar, you can obtain the hg38 FASTA file here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

The all_loci.bed file is generated from this by RepeatFinder (included with MANTIS).

Answer 5 · 2019-03-29T05:58:25.000Z

When I run the following command as mentioned on Github, it says command not found. I even tried going into the tools folder within MANTIS-master and running it. I dont see any file named repeatfinder. Please advise. ./RepeatFinder –i /path/to/genome.fasta -o /path/to/loci.bed Sincerely, Akshata

…

On Mar 28, 2019, 9:15 AM -0700, rbonneville ***@***.***>, wrote: Hello @audyavar, you can obtain the hg38 FASTA file here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz The all_loci.bed file is generated from this by RepeatFinder (included with MANTIS). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

Answer 6 · 2019-03-29T06:09:40.000Z

This doesn’t seem to compile on Mac OSX. I tried various approaches below based on C++ compiling instructions on the web. See the log below. [tools]$./Makefile ./Makefile: line 5: all:: command not found ./Makefile: line 7: RepeatFinder:: command not found clang: error: no input files ./Makefile: line 8: LDFLAGS: command not found ./Makefile: line 8: main.o: command not found error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip: can't open file: RepeatFinder (No such file or directory) ./Makefile: line 11: main.o:: command not found clang: error: no input files ./Makefile: line 12: CFLAGS: command not found ./Makefile: line 12: -c: command not found ./Makefile: line 14: circularLinkedList.o:: command not found clang: error: no input files ./Makefile: line 15: CFLAGS: command not found ./Makefile: line 15: -c: command not found ./Makefile: line 17: clean:: command not found [tools]$make Makefile make: Nothing to be done for `Makefile’. [tools]$./Makefile ./Makefile: line 5: all:: command not found ./Makefile: line 7: RepeatFinder:: command not found clang: error: no input files ./Makefile: line 8: LDFLAGS: command not found ./Makefile: line 8: main.o: command not found error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip: can't open file: RepeatFinder (No such file or directory) ./Makefile: line 11: main.o:: command not found clang: error: no input files ./Makefile: line 12: CFLAGS: command not found ./Makefile: line 12: -c: command not found ./Makefile: line 14: circularLinkedList.o:: command not found clang: error: no input files ./Makefile: line 15: CFLAGS: command not found ./Makefile: line 15: -c: command not found ./Makefile: line 17: clean:: command not found [tools]$gcc main.cpp -o main.out Undefined symbols for architecture x86_64: "mantis::CircularLinkedList::endSequence()", referenced from: _main in main-a60901.o "mantis::CircularLinkedList::nextNoResultCheck(char const&)", referenced from: _main in main-a60901.o "mantis::CircularLinkedList::next(char const&)", referenced from: _main in main-a60901.o "mantis::CircularLinkedList::CircularLinkedList(int, int, int, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from: _main in main-a60901.o "mantis::CircularLinkedList::~CircularLinkedList()", referenced from: _main in main-a60901.o "mantis::CircularLinkedList::getLastLength() const", referenced from: outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o "mantis::CircularLinkedList::getRepeatCount() const", referenced from: outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o "mantis::CircularLinkedList::getKmer() const", referenced from: outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o "std::__1::locale::has_facet(std::__1::locale::id&) const", referenced from: bool std::__1::has_facet<std::__1::codecvt<char, char, __mbstate_t> >(std::__1::locale const&) in main-a60901.o "std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from: std::__1::ctype<char> const& std::__1::use_facet<std::__1::ctype<char> >(std::__1::locale const&) in main-a60901.o std::__1::codecvt<char, char, __mbstate_t> const& std::__1::use_facet<std::__1::codecvt<char, char, __mbstate_t> >(std::__1::locale const&) in main-a60901.o "std::__1::ios_base::getloc() const", referenced from: std::__1::basic_ios<char, std::__1::char_traits<char> >::widen(char) const in main-a60901.o "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(char const*, unsigned long)", referenced from: std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string<std::__1::nullptr_t>(char const*) in main-a60901.o "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(unsigned long, char)", referenced from: std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(unsigned long, char) in main-a60901.o "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::assign(char const*)", referenced from: std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::operator=(char const*) in main-a60901.o "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::push_back(char)", referenced from: std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::operator+=(char) in main-a60901.o "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from: _main in main-a60901.o "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_string()", referenced from: _main in main-a60901.o outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in main-a60901.o "std::__1::basic_istream<char, std::__1::char_traits<char> >::get()", referenced from: std::__1::basic_istream<char, std::__1::char_traits<char> >::get(char&) in main-a60901.o "std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from: construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from: construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from: std::__1::basic_ifstream<char, std::__1::char_traits<char> >::basic_ifstream(char const*, unsigned int) in main-a60901.o std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::put(char)", referenced from: std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::flush()", referenced from: std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::endl<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::sentry(std::__1::basic_ostream<char, std::__1::char_traits<char> >&)", referenced from: std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::~sentry()", referenced from: std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from: construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from: construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from: std::__1::basic_ofstream<char, std::__1::char_traits<char> >::basic_ofstream(char const*, unsigned int) in main-a60901.o std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(int)", referenced from: outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned long)", referenced from: outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::uflow()", referenced from: vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsgetn(char*, long)", referenced from: vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsputn(char const*, long)", referenced from: vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::showmanyc()", referenced from: vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in main-a60901.o "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::basic_streambuf()", referenced from: std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in main-a60901.o "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::~basic_streambuf()", referenced from: std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in main-a60901.o "std::__1::cerr", referenced from: _main in main-a60901.o "std::__1::cout", referenced from: _main in main-a60901.o "std::__1::ctype<char>::id", referenced from: std::__1::ctype<char> const& std::__1::use_facet<std::__1::ctype<char> >(std::__1::locale const&) in main-a60901.o "std::__1::locale::locale(std::__1::locale const&)", referenced from: std::__1::basic_streambuf<char, std::__1::char_traits<char> >::getloc() const in main-a60901.o "std::__1::locale::~locale()", referenced from: std::__1::basic_ios<char, std::__1::char_traits<char> >::widen(char) const in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in main-a60901.o "std::__1::codecvt<char, char, __mbstate_t>::id", referenced from: std::__1::codecvt<char, char, __mbstate_t> const& std::__1::use_facet<std::__1::codecvt<char, char, __mbstate_t> >(std::__1::locale const&) in main-a60901.o bool std::__1::has_facet<std::__1::codecvt<char, char, __mbstate_t> >(std::__1::locale const&) in main-a60901.o "std::__1::ios_base::__set_badbit_and_consider_rethrow()", referenced from: std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in main-a60901.o "std::__1::ios_base::init(void*)", referenced from: std::__1::basic_ios<char, std::__1::char_traits<char> >::init(std::__1::basic_streambuf<char, std::__1::char_traits<char> >*) in main-a60901.o "std::__1::ios_base::clear(unsigned int)", referenced from: std::__1::ios_base::setstate(unsigned int) in main-a60901.o "std::__1::basic_ios<char, std::__1::char_traits<char> >::~basic_ios()", referenced from: std::__1::basic_ifstream<char, std::__1::char_traits<char> >::basic_ifstream(char const*, unsigned int) in main-a60901.o std::__1::basic_ofstream<char, std::__1::char_traits<char> >::basic_ofstream(char const*, unsigned int) in main-a60901.o std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in main-a60901.o std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in main-a60901.o "std::bad_cast::bad_cast()", referenced from: std::__1::__throw_bad_cast() in main-a60901.o "std::bad_cast::~bad_cast()", referenced from: std::__1::__throw_bad_cast() in main-a60901.o "std::terminate()", referenced from: ___clang_call_terminate in main-a60901.o "typeinfo for std::__1::basic_istream<char, std::__1::char_traits<char> >", referenced from: construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o typeinfo for std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o "typeinfo for std::__1::basic_ostream<char, std::__1::char_traits<char> >", referenced from: construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o typeinfo for std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o "typeinfo for std::__1::basic_streambuf<char, std::__1::char_traits<char> >", referenced from: typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in main-a60901.o "typeinfo for std::bad_cast", referenced from: std::__1::__throw_bad_cast() in main-a60901.o "vtable for __cxxabiv1::__si_class_type_info", referenced from: typeinfo for std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in main-a60901.o typeinfo for std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o NOTE: a missing vtable usually means the first non-inline virtual member function has no definition. "vtable for std::__1::ios_base", referenced from: std::__1::ios_base::ios_base() in main-a60901.o NOTE: a missing vtable usually means the first non-inline virtual member function has no definition. "vtable for std::__1::basic_ios<char, std::__1::char_traits<char> >", referenced from: std::__1::basic_ios<char, std::__1::char_traits<char> >::basic_ios() in main-a60901.o NOTE: a missing vtable usually means the first non-inline virtual member function has no definition. "virtual thunk to std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from: construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o "virtual thunk to std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from: construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in main-a60901.o "virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from: construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o "virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from: construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in main-a60901.o "operator delete[](void*)", referenced from: _main in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::setbuf(char*, long) in main-a60901.o "operator delete(void*)", referenced from: _main in main-a60901.o std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in main-a60901.o std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in main-a60901.o "operator new[](unsigned long)", referenced from: _main in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::setbuf(char*, long) in main-a60901.o "operator new(unsigned long)", referenced from: _main in main-a60901.o "___cxa_allocate_exception", referenced from: std::__1::__throw_bad_cast() in main-a60901.o "___cxa_begin_catch", referenced from: ___clang_call_terminate in main-a60901.o std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in main-a60901.o "___cxa_call_unexpected", referenced from: std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >::ostreambuf_iterator(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) in main-a60901.o std::__1::unique_ptr<__sFILE, int (*)(__sFILE*)>::reset(__sFILE*) in main-a60901.o bool std::__1::has_facet<std::__1::codecvt<char, char, __mbstate_t> >(std::__1::locale const&) in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::__make_mdstring(unsigned int) in main-a60901.o "___cxa_end_catch", referenced from: std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in main-a60901.o std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in main-a60901.o "___cxa_throw", referenced from: std::__1::__throw_bad_cast() in main-a60901.o "___gxx_personality_v0", referenced from: _main in main-a60901.o std::__1::basic_ifstream<char, std::__1::char_traits<char> >::basic_ifstream(char const*, unsigned int) in main-a60901.o std::__1::basic_ofstream<char, std::__1::char_traits<char> >::basic_ofstream(char const*, unsigned int) in main-a60901.o outputLocus(mantis::CircularLinkedList*, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long) in main-a60901.o std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in main-a60901.o std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in main-a60901.o std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in main-a60901.o ... ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) Sincerely, Akshata

…

On Mar 28, 2019, 10:58 PM -0700, Akshata Udyavar ***@***.***>, wrote: When I run the following command as mentioned on Github, it says command not found. I even tried going into the tools folder within MANTIS-master and running it. I dont see any file named repeatfinder. Please advise. ./RepeatFinder –i /path/to/genome.fasta -o /path/to/loci.bed Sincerely, Akshata On Mar 28, 2019, 9:15 AM -0700, rbonneville ***@***.***>, wrote: > Hello @audyavar, you can obtain the hg38 FASTA file here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz > The all_loci.bed file is generated from this by RepeatFinder (included with MANTIS). > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub, or mute the thread.

Answer 7 · 2019-04-02T19:31:10.000Z

Hi @audyavar,

MANTIS (and RepeatFinder) are only officially supported on Linux, but you may be able to compile it on a Mac with these commands.

g++ -c main.cpp -o main.o
g++ -c circularLinkedList.cpp -o circularLinkedList.o
g++ main.o circularLinkedList.o -o RepeatFinder

Answer 8 · 2019-04-18T14:39:56.000Z

Hello, I couldn’t see this comment on github for some reason, but this error is most likely because you have a hyphen in "–i" rather than a dash like in "-o". Russell From: Akshata Udyavar [mailto:notifications@github.com] Sent: Wednesday, April 17, 2019 8:27 PM To: OSU-SRLab/MANTIS <MANTIS@noreply.github.com> Cc: Bonneville, Russell <Russell.Bonneville@osumc.edu>; State change <state_change@noreply.github.com> Subject: Re: [OSU-SRLab/MANTIS] Microsatellite Loci BED File (#40) I tried running the following commands, but it keeps saying “must supply input FASTA”. I tried the hg38.fa.gz file initially (downloaded from the link in the previous email), then I unzipped it, still the same error. Please advice. ./RepeatFinder –i /mnt/mantis/MANTIS-master/hg38/hg38.fa -o /mnt/mantis/MANTIS-master/loci.bed ERROR: Must supply input FASTA. Sincerely, Akshata

Answer 9 · 2019-07-18T09:52:10.000Z

Hi
I tried to create bed file as mentioned in MANTIS manual. But I couldnt find Repeatfinder tool in the MANTIS. Can u suggest me for creating bed file? Thanks in advance.

Answer 10 · 2019-07-18T14:55:17.000Z

Hi @YuvaraniThambidurai,

The RepeatFinder source is included in the MANTIS distribution. To compile it on Linux, simply run make in the tools directory.

Answer 11 · 2019-07-19T07:42:31.000Z

Hi As per the above instructions I would be able to generate the BED file. Thanks much. Regards, Yuvarani

…

On Thu, Jul 18, 2019 at 8:25 PM rbonneville ***@***.***> wrote: Hi @YuvaraniThambidurai <https://github.com/YuvaraniThambidurai>, The RepeatFinder source is included in the MANTIS distribution. To compile it on Linux, simply run make in the tools directory. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#40?email_source=notifications&email_token=AMUVJRAUMWZNCEDLNN3FNITQAB75NA5CNFSM4FWYGBNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2IXZWQ#issuecomment-512851162>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMUVJRDEEAP5DUBWETUAKRDQAB75NANCNFSM4FWYGBNA> .

-- The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future.