Dear all,
I am trying to run SICER on my files. I have done a bamToBed conversion and concatanated the files with cat.
Command looks like:
SICER.sh . merged.bed ctl.bam.bed . mm10 1 200 50 0.83 600 0.01
What Sicer does is it produces two big "removed" files and all the other files are empty. and no bedfiles.
this is the out:
m Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
m Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
1 Plus reads: 21272531 Retained plus reads: 18711806 ; Minus reads: 21284872 Retained minus reads: 18718548
0 Plus reads: 18979534 Retained plus reads: 16908229 ; Minus reads: 19025034 Retained minus reads: 16934977
_ Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
c Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
h Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
r Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
o Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
m Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
s Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
No idea what m,c,r,h etc. reads are..
thanks, we have added mm10 and hg38 to genomedata.py previously. So i believe its not the problem.
Any idea what is an m read?
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Hi, Indeed there was a problem with the genomedata.py. As you see the chromosomes spell our mm10-chroms :) thanks!