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.
