Each run generate different result

Question

[huangbin]

My code is the following below:

#---------------------------------
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
#---------------------------------
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
#---------------------------------
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.

[lieven.sterck]

Hello huangbin,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!