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Forum: Ion Torrent 06-10-2013, 07:25 AM
Replies: 3
Views: 5,668
Posted By vpp605
Removing Duplicate Reads from Torrent data

Does anyone have any experience with removing duplicate reads from Ion Torrent data? Any idea if the 454-designed programs work well with Torrent (e.g., cd-hit-454)? Or any suggestions for other...
Forum: Literature Watch 04-18-2013, 09:52 AM
Replies: 29
Views: 22,895
Posted By vpp605
Ray Meta - taxonomy and gene ontology


I have a general question about the way Ray Meta works. When the taxonomy and gene ontology profiles are provided, I assume that is only for the assembled contigs? Or would that also...
Forum: Bioinformatics 11-28-2012, 04:03 PM
Replies: 9
Views: 2,469
Posted By vpp605
I have a follow-up question regarding the comment...

I have a follow-up question regarding the comment "Why are you separating the up and down into separate lists?".
Is there a way to see what GO terms are enriched in the up-regulated, and in the...
Forum: Bioinformatics 07-06-2011, 04:04 PM
Replies: 5
Views: 4,652
Posted By vpp605
similar cuffmerge problem

I am having a similar problem, where I have transcripts that do not show up in my merged file. I can find the transcripts (and associated FPKM's) in both original gtf files that I am trying to merge,...
Forum: RNA Sequencing 11-29-2010, 06:04 AM
Replies: 15
Views: 23,494
Posted By vpp605
Thank you everyone for the replies!! ...

Thank you everyone for the replies!!

golharam - thank you for pointing me to that paper!

Simon - sorry for making you repeat everything over again -- if there is a "better" post for me to look...
Forum: RNA Sequencing 11-16-2010, 04:00 PM
Replies: 15
Views: 23,494
Posted By vpp605
Biological replicates for RNA-seq

Hi all,

I'm not sure if this has already been discussed elsewhere, but after looking around I didn't find anything directly answering my question, so if it has already been discussed, sorry for...
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