Deleted:Generate a count matrix for a consensus peak set and related peaks/reads
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Entering edit mode
6 weeks ago
Farzaneh • 0

Hi everyone, I have a consensus peak file (.bed) that have, Chr, start, end. It doesn't have any header. Something like this:

chr1    721000  726999
chr1    817800  821799
chr1    1027400 1030799
chr1    1033600 1037599
chr1    1047400 1050399

I want to generate a count matrix for my downstream analysis and differential analysis. Basically, compare this consensus peak file with my .bam read files to have how many (fragment) of reads I get in each peak.

The code I used to make by .bam to .saf was:

awk 'OFS="\t" {print $1"."$2"."$3, $1, $2, $3}' Consensus.bed > Consensus.saf

This is what it returns: which I'm not sure if it's correct or not.

> chr1.721200.726999    chr1    721200  726999
> chr1.819000.821399    chr1    819000  821399
> chr1.926400.928399    chr1    926400  928399
> chr1.1033800.1037799  chr1    1033800 1037799
> chr1.1047800.1050199  chr1    1047800 1050199

This is featureCounts I'm using

featureCounts -T 8 -a Consensus.saf -F SAF -o Dinput.txt HCT116_Input.bam HCT116_1.bam HCT116_2.bam HCT116_3.bam

That gives me the error of:

ERROR: no features were loaded in format GTF. The annotation format can be specified by the '-F' option, and the required feature type can be specified by the '-t' option

Can someone please help me writing the codes I need to get to what I want? It's been a while I stuck and have no one to get further help. I'd really appreciate it.

Chipseq countmatrix featureCounts • 138 views
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