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Forum: Bioinformatics 02-14-2014, 12:22 PM
Replies: 1
Views: 905
Posted By wonaya
QC for replicates in ChIP-seq

Hi, I have some ChIP-seq data to QC.
I was browsing for a pipeline where you can compare between biological replicates for their similarities, but haven't had any luck.
Is there a standard...
Forum: Bioinformatics 02-06-2014, 12:53 PM
Replies: 5
Views: 1,454
Posted By wonaya
Thanks, Actually, it did warn me of Obs/Exp...

Thanks,

Actually, it did warn me of Obs/Exp Max being 58 for some. I was thinking of trimming the ends, perhaps at 121bp, but the results for forward strands seems fine. I may just go ahead with...
Forum: Bioinformatics 02-06-2014, 11:52 AM
Replies: 5
Views: 1,454
Posted By wonaya
Strange kmer patterns in FastQC results

Hi,
I need help in interpreting the fastQC results I have on my sample from paired-end ChIP-seq (151bp long from miseq)

After removing adapter sequences using trim-galore, I am still seeing...
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