TelSeq is a software that estimates telomere length from whole genome sequencing data (BAMs). The most current development version is available from our git repository: git://github.com/zd1/telseq.git The software is implemented in C++. We also have a Python implementation. But it is not updated anymore. You could switch to branch 'python' using the 'branch' button above and follow the instructions there. Precompiled executables ============================ For Mac OSX bin/mac/telseq For linux bin/linux/telseq Compiling TelSeq ============================ TelSeq dependency: -------------------------------- - the bamtools library (https://github.com/pezmaster31/bamtools) Compiling --------------------------- Go to the src directory and run autogen.sh from the src directory to generate the configure file ./autogen.sh Then run ./configure make The executable binary will be at src/Telseq/telseq If bamtools are installed not at the system location, you can specify their location by ./configure --with-bamtools=/path/to/bamtools The /path/to/bamtools directory is the directory that contains 'lib' and 'include' sub directories. Running TelSeq ============================= # Read options and usage information --------------------------- > telseq # Analyse one or more BAMs by specifying BAM file path as command line arguments. --------------------------- > telseq a.bam b.bam # Analyse a list of BAMs whose paths are specified in a 'bamlist' file. --------------------------- bamlist should contain only 1 column with each row the path of a BAM. i.e. /path/to/a.bam /path/to/b.bam > telseq -f bamlist # BAM file path can also be provided by piping in a 'bamlist', whose format must be # same as above --------------------------- > cat bamlist | telseq # output --------------------------- By default the result will be printed out to stdout. To change it to a file, use '-o' option to specify a file path. i.e. > telseq -o /path/to/output a.bam b.bam c.bam This can also be achived by just direct the output to a file using '>', i.e. > telseq a.bam b.bam c.bam > /path/to/output The software will print out running status to stderr as well. To separate them from stdout, one could direct log to a file, ie. > telseq a.bam b.bam c.bam 2>outputlog # output file format --------------------------- # column definations ReadGroup: read group the result is corresponding to. Defined by the RG tag in BAM header. Library: sequencing library that the read group belongs to. Sample: defined by the SM tag in BAM header. Total: total number of reads in this read group. Mapped: total number of mapped reads in this read group. Wether a read is mapped is determined by SAM flag 0x4. Duplicates: total number of duplicate reads in this read group. Wether a read is a duplicate is determined by SAM flag 0x400. LENGH_ESTIMATE: estimated telomere length TEL0: read counts for reads containing no TTAGGG/CCCTAA repeats. TEL1: read counts for reads containing only 1 TTAGGG/CCCTAA repeats. TELn: read counts for reads containing only n TTAGGG/CCCTAA repeats. TEL16: read counts for reads containing 16 TTAGGG/CCCTAA repeats. GC0: read counts for reads with GC composition between 40%-42%, GC1: read counts for reads with GC composition between 42%-44%, GCn: read counts for reads with GC composition between (40%+n*2%)-(42%+(n+1)*2%), GC9: read counts for reads with GC composition between 58%-60%, By default for each BAM a header line will be printed out. This can be suppressed by using the '-H' option. It is useful when one has multiple BAMs to scan and wish the output to be merged together. i.e. > telseq -H a.bam b.bam c.bam > myresult To just print out the header, use '-h' option. i.e. > telseq -h