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Forum: Bioinformatics 12-02-2015, 03:34 PM
Replies: 1
Views: 3,080
Posted By pshah
htseq-count failure parsing GFF attribute line

Hi,
I am trying to generate a read counts file for my ChIP-seq data using htseq-count. Here is what I have done so far:

1. Call ChIP-seq peaks and output BED file in MACS2
2. Convert BED to GFF...
Forum: Epigenetics 09-08-2015, 11:34 AM
Replies: 2
Views: 1,674
Posted By pshah
Thanks for your input, Chipper. It's good to know...

Thanks for your input, Chipper. It's good to know that this is a fairly common problem.

I do get some nice peak calling using MACS2. I will have to take a closer look at those peaks to see if I...
Forum: Epigenetics 09-04-2015, 03:43 PM
Replies: 2
Views: 1,674
Posted By pshah
Unhappy Input giving peak at TSS! Yikes!

Hi all,
It's my first attempt at ChIP-seq. I optimized fixation time, shearing, IP. I confirmed my ChIP was working by qPCR. Prepped libraries and sequenced on a HiSeq 1500 (SE, 50 cycles to start...
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