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Forum: Epigenetics 01-24-2013, 11:23 AM
Replies: 10
Views: 3,264
Posted By DunderChief
Is my chip-seq data garbage?

I received some chip-seq data that had a very high amount of sequence duplication (over 90% of the reads). The experiment was looking at H3K4me3. I aligned with bowtie2 and ran rmdup and ended up...
Forum: Bioinformatics 11-27-2012, 06:58 AM
Replies: 11
Views: 2,333
Posted By DunderChief
All of this is explained in detail on the...

All of this is explained in detail on the trimmomatic website (http://www.usadellab.org/cms/index.php?page=trimmomatic), but in general this will:

1. Clip Illumina adapters
2. then trim the...
Forum: Bioinformatics 11-20-2012, 10:07 AM
Replies: 5
Views: 2,073
Posted By DunderChief
I would be cautious about switching to solexa...

I would be cautious about switching to solexa scores just because you get a higher alignment rate. It seems like you have a problem unrelated to your quality scores and you'll probably end up...
Forum: Bioinformatics 11-15-2012, 07:38 AM
Replies: 4
Views: 967
Posted By DunderChief
You have a ton of sequences with <3 for average...

You have a ton of sequences with <3 for average quality. Remove these sequences, and re-run the fastQC. You may have enough sequences to salvage something.
Forum: Bioinformatics 10-19-2012, 09:20 AM
Replies: 12
Views: 7,423
Posted By DunderChief
Thanks Wallysb01, that's propably it. I am using...

Thanks Wallysb01, that's propably it. I am using a soft-masked reference (low complexity regions are lowercase).
Forum: Bioinformatics 10-19-2012, 07:43 AM
Replies: 12
Views: 7,423
Posted By DunderChief
-------bump------- I also get this using...

-------bump-------

I also get this using Ensembl human reference (v. 68)
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