SICER fails to run

Question

[ildem]

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..

[ildem]

Hi, Indeed there was a problem with the genomedata.py. As you see the chromosomes spell our mm10-chroms :) thanks!

Answer 1

[aka001]

I would suspect that mm10 genome information is not in your system yet. You can first start by checking the GenomeData.py file inside the lib directory of SICER and see if mm10 info is there or not.

[Nil Desperandum]

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?