Entering edit mode
2.9 years ago
huangbin
•
0
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.
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!