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Forum: Bioinformatics 03-21-2016, 06:47 AM
Replies: 1
Views: 1,271
Posted By genomica
rRNA removal for RNAseq analysis

Hi all,

Do you think we need to filter rRNA and low complexity reads from Poly-A selected total mRNAseq stranded data before performing RNAseq analysis (tophat2-htseq-deseq2)? I am sorry if I...
Forum: Bioinformatics 10-23-2015, 05:31 AM
Replies: 3
Views: 1,404
Posted By genomica
Sorry about that, Michael. I will keep this in...

Sorry about that, Michael. I will keep this in mind. :)
Forum: Bioinformatics 10-22-2015, 03:16 AM
Replies: 3
Views: 1,404
Posted By genomica
Please ignore the previous post. It was my bad in...

Please ignore the previous post. It was my bad in noting the versions of Deseq2. Its v1.2.10 for R3.0.2 and v1.10 for R3.2.0. Sorry!
Forum: Bioinformatics 10-22-2015, 02:04 AM
Replies: 3
Views: 1,404
Posted By genomica
Deseq2 results discrepancies because of versions of R

Hello all,

I was asked to repeat RNAseq analysis done a while ago. Previously, analysis was done using Deseq2 v1.2.10 and R v.3.0.2. Although we are still using the same version for Deseq2, R on...
Forum: Bioinformatics 09-26-2015, 02:03 AM
Replies: 6
Views: 1,869
Posted By genomica
Thanks a lot for your help Devon.

Thanks a lot for your help Devon.
Forum: Bioinformatics 09-25-2015, 12:31 AM
Replies: 6
Views: 1,869
Posted By genomica
Thanks very much Devon. Yes, I did figure out the...

Thanks very much Devon. Yes, I did figure out the first error :)

I am a bit paranoid as I am doing this analysis for the first time and hence wondered if you could confirm if my experimental...
Forum: Bioinformatics 09-24-2015, 07:38 AM
Replies: 6
Views: 1,869
Posted By genomica
Thanks for the hint, that's really helpful. So, I...

Thanks for the hint, that's really helpful. So, I understand if I want to get comparison of conditions considering the pairing of samples into account, I should give


res <- results(dds,...
Forum: Bioinformatics 09-24-2015, 06:47 AM
Replies: 6
Views: 1,869
Posted By genomica
Deseq2 multifactor analysis

Hello,

I have a RNAseq experiment where I have 2 conditions and 3 replicates each and replicates are taken from different individuals. So my design is as follows:

Sample Condition Individual...
Forum: Bioinformatics 02-13-2013, 07:26 AM
Replies: 0
Views: 1,384
Posted By genomica
GSNAP Error message "splicesites file has a negative distance"

Hello,

I am working with an RNASeq project and am trying to use GSNAP for the same. Splicesites are created with a few warning messages using gff3_splicesites from GMAP package. However, when I...
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