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Search: Posts Made By: habbas
Forum: Bioinformatics 12-30-2015, 10:54 PM
Replies: 0
Views: 1,626
Posted By habbas
How to customize cufflinks output COLUMNS

Hi-
I am running cufflinks on mouse RNAseq with genes.gtf as reference file on the bam files that i generated using tophat2/bowtie. The output genes.fpkm_tracking and isoforms.fpkm_tracking have the...
Forum: Bioinformatics 01-28-2015, 09:13 AM
Replies: 5
Views: 2,924
Posted By habbas
Hi Gordon- Thanks for your reply. I am a...

Hi Gordon- Thanks for your reply.
I am a beginner in this. I know how to use DESeq2 to analyze RNASeq data from tables generated by summarizeOverlaps function. I was wondering how would your...
Forum: Bioinformatics 01-27-2015, 08:25 AM
Replies: 5
Views: 2,924
Posted By habbas
Hi - Were you able to find a solution to this...

Hi -
Were you able to find a solution to this problem?
Forum: Bioinformatics 12-30-2014, 06:41 AM
Replies: 4
Views: 1,862
Posted By habbas
I posted the question on the support website of...

I posted the question on the support website of bioconductor and found a solution for the problem. Here's the link for it:

https://support.bioconductor.org/p/63875/#63902
Forum: Bioinformatics 12-29-2014, 07:45 AM
Replies: 4
Views: 1,862
Posted By habbas
Here's my sessionInfo(). Does it look right? ...

Here's my sessionInfo(). Does it look right?

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1]...
Forum: Bioinformatics 12-29-2014, 07:40 AM
Replies: 4
Views: 1,862
Posted By habbas
Thank you for your reply. I am using the latest R...

Thank you for your reply. I am using the latest R version. I am not sure what's the difference between the two links you provided above. They both seem to link to the same downloadable links:
...
Forum: Bioinformatics 12-23-2014, 06:32 AM
Replies: 4
Views: 1,862
Posted By habbas
summarizeOverlaps too, too slow then freeze

I hope someone can help in this issue.


I have 8 bam files from mm9 alignment, each ~4-5 geg in size. When I run summarizeOverlaps over 3 files, it takes 2-3 hours to finish and it works although...
Forum: Bioinformatics 11-02-2014, 07:21 PM
Replies: 0
Views: 1,147
Posted By habbas
addFeatures not working on cummerbund

Hi- I am trying to addFeatures column via cummerBund. I have tried the script on my friend's computer and it works fine. but, it doesn't seem to add anything on mine. It does not even show me any...
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