--strandfile

Question

--strandfile

Opened this issue 6 years ago · 8 comments

Hi,
I'm trying to convert alleles coding from forward type to top but i do not know how to construct the strandfile for my data? I have data from a sample of sheep genotyped with the illumina 50OvineBeadchip
thanks in advance

Sara

Answer 1 · 2018-10-12T13:44:07.000Z

strand file is only needed if you have dbSNP data and if the dbSNP data for that particular SNP is not on forward strand (due to genome assembly differences over time). In your case, there is no need to use strand file, just follow instructions in the website.

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On Fri, Oct 12, 2018 at 6:17 AM racheese ***@***.***> wrote: Hi, I'm trying to convert alleles coding from forward type to top but i do not know how to construct the strandfile for my data? I have data from a sample of sheep genotyped with the illumina 50OvineBeadchip thanks in advance Sara — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuJwK5nLhYxVW3MJTS83yez3cPUfHks5ukGw5gaJpZM4XZMoQ> .

Answer 2 · 2018-10-15T09:30:20.000Z

Thank you for the answer, I tryied to follow instructions:

convert_bim_allele.pl /home/sara/GenGen-1.0.1/testcomisana.bim /home/sara/GenGen-1.0.1/test/SNPTable.txt -intype forward -outtype top -outfile /home/sara/GenGen-1.0.1/testcomisana.top.bim

but I got the following answer
Error in argument: please specify --strandfile when '-intype' is 'forward'

I'ma almost sure that my current coding is not Top

Answer 3 · 2019-02-27T15:26:59.000Z

Hi!

I have the same problem. I am trying to convert an Illumina export file (TOPBOT) to forward strand, and is asked for a strandfile. In the instruction, it says to use the snp14 file and cut the appropriate columns. What is a snp14 file and what is the appropriate columns?

Thanks

Answer 4 · 2019-02-27T15:39:00.000Z

This means UCSC's dbsnp build. Their name is typically snp14*, for example, http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp147.txt.gz. It is tab-delimited file and the strand information is in one of the columns.

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On Wed, Feb 27, 2019 at 10:27 AM sboerte ***@***.***> wrote: Hi! I have the same problem. I am trying to convert an Illumina export file (TOPBOT) to forward strand, and is asked for a strandfile. In the instruction, it says to use the snp14 file and cut the appropriate columns. What is a snp14 file and what is the appropriate columns? Thanks — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuCywD4Etos5hSZr66SSx_8wXYKVdks5vRqPEgaJpZM4XZMoQ> .

Answer 5 · 2019-02-27T16:05:55.000Z

Thanks for clearyfying! Just extracting chr, pos, rs and +/- then? (there are no headers in the file)
Would it be possible, somehow, to specify a file with information about the reference and alternative alleles, in addition to top/bot strand instead? I have a mapping file, run with blat, that has used hg19 as reference, and the resulting file containts information about TOPBOT-strand, ref/alt alleles according to TOPBOT and ref/alt alleles according to forward strand (hg19)

Thanks

Answer 6 · 2020-02-21T18:44:31.000Z

@kaichop

Is it specified anywhere what is the correct format for the strandfile? I did not find this in the documentation and I am not working on human data.

Which columns need to appear in the strandfile?

It seems that I can't run GenGen without specifying a strandfile:

Error in argument: please specify --strandfile when '-outtype' is 'forward'

Answer 7 · 2020-02-21T18:52:42.000Z

You can build such a file yourself, it is just a simple two-column file with SNP and the strand (+ or -). For example, if you download the dbSNP file from UCSC, you can cut these two columns out from many columns, but there are many other ways to get the strand for the rs identifiers from other sources.

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On Fri, Feb 21, 2020 at 1:44 PM amizeranschi ***@***.***> wrote: @kaichop <https://github.com/kaichop> Is it specified anywhere what is the correct format for the strandfile? I did not find this in the documentation and I am not working on human data. Which columns need to appear in the strandfile? It seems that I can't run GenGen without specifying a strandfile: Error in argument: please specify --strandfile when '-outtype' is 'forward' — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABNG3OB3FQ2I5R7DDCTCMH3REAOI7A5CNFSM4F3EZIIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMTV5KI#issuecomment-589782697>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OB3WWWP3HFTP362DCLREAOI7ANCNFSM4F3EZIIA> .

Answer 8 · 2020-02-21T19:08:06.000Z

Alright, thanks for the quick answer!