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Forum: RNA Sequencing 07-24-2015, 06:20 AM
Replies: 4
Views: 2,922
Posted By chumho
Thanks. It makes sense now.

Thanks. It makes sense now.
Forum: RNA Sequencing 07-23-2015, 10:13 AM
Replies: 4
Views: 2,922
Posted By chumho
Thanks cmbetts for the reply. I agree that...

Thanks cmbetts for the reply.

I agree that "The tophat output says that 17.7% of your reads ~10M have multiple alignments. Those will all get counted as _alignment_no_unique since they can't be...
Forum: RNA Sequencing 07-23-2015, 08:41 AM
Replies: 4
Views: 2,922
Posted By chumho
htseq-count __alignment_not_unique vs tophat

Hi guys,

I'm really confused by the numbers between tophat & htseq-count.

There was a huge difference between __alignment_not_unique from htseq-count and unmapped reads from tophat. Here's the...
Forum: Bioinformatics 05-02-2013, 10:21 AM
Replies: 10
Views: 4,562
Posted By chumho
VarScan2 copynumber crashed

I encountered the same problem for VarScan 2.3.5 on Linux. Any clue?
Eric.
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