Sicer peak calling
1
0
Entering edit mode
18 months ago
aropri ▴ 80

Has anyone used Sicer to peak call using bam files and bed files. I would appreciate it if someone could help me get the command to do peak calling using treatment vs input bam files. Also, how does sicer use bed files to peak call, i thought peak calling was produced bed files. Would appreciate any help.

ChIP-Seq • 1.1k views
ADD COMMENT
1
Entering edit mode
18 months ago

Have you read the manual? It gives very clear commands as for how to run with a control file (or without):

sicer -t treatment.bam -c control.bam -s hg38 -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 -g 600 -e 1000

Those are the default parameters. You can supply the reads in either bam or BED format. Having aligned reads in BED format isn't too uncommon.

The output files are in BED-like format, you can read more about them here.

ADD COMMENT
0
Entering edit mode

Thank you so much. I did look at the documentation, I was running that command with my bam files but not getting any peaks.

ADD REPLY
0
Entering edit mode

So are you still running into issues or were you just a bit confused about the input/output?

ADD REPLY
0
Entering edit mode

I figured it out, no issues now. I converted bam file to bed and added chr as a prefix and it ran fine. Thank you so much!

ADD REPLY

Login before adding your answer.

Traffic: 2956 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6