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genome-vendor / bsmap

Unofficial repo for software vendoring or packaging purposes
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Each run generate different result #9

Open Huangbin8 opened 3 years ago

Huangbin8 commented 3 years ago

My code is the following below:

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bsmap -a /public/workspace/huangbin/WGBS/1.rawdata/M_FDLM210080249-1a/M_FDLM210080249-1a_1.fq.gz \ -b /public/workspace/huangbin/WGBS/1.rawdata/M_FDLM210080249-1a/M_FDLM210080249-1a_2.fq.gz \ -d /public/workspace/huangbin/WGBS_ref/hg19/hg19.fa \ -o Mrst.bam -p 15 -w 100 -v 5

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samtools sort -@ 8 /public/workspace/huangbin/WGBS/bsmaprst/M/Mrst.bam -o /public/workspace/huangbin/WGBS/bsmaprst/M/Mrst.sorted.bam samtools index /public/workspace/huangbin/WGBS/bsmaprst/M/Mrst.sorted.bam

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python /public/workspace/huangbin/WGBS/bsmaprst/methratio.py \ -o /public/workspace/huangbin/WGBS/bsmaprst/M/methratio_M.txt \ -d /public/workspace/huangbin/WGBS_ref/hg19/hg19.fa \ /public/workspace/huangbin/WGBS/bsmaprst/M/Mrst.sorted.bam

some difference of "pos", "ratio", "total_C", "methy_C" in methratio_M.txt. The Mrst.bam file produced in the first step has inconsistent file sizes each time it is run with the same parameters.

chrisamiller commented 3 years ago

This repository is a fork of the main bsmap project for convenience. We didn't write it and no longer use it, so unfortunately can't be much help.