Question: Sicer peak calling
0
gravatar for aropri
5 weeks ago by
aropri0
aropri0 wrote:

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 • 116 views
ADD COMMENTlink modified 5 weeks ago by jared.andrews076.4k • written 5 weeks ago by aropri0
0
gravatar for jared.andrews07
5 weeks ago by
jared.andrews076.4k
Memphis, TN
jared.andrews076.4k wrote:

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 COMMENTlink written 5 weeks ago by jared.andrews076.4k

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 REPLYlink written 5 weeks ago by aropri0

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

ADD REPLYlink written 5 weeks ago by jared.andrews076.4k

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 REPLYlink written 26 days ago by aropri0
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