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Forum: RNA Sequencing 10-29-2013, 10:56 AM
Replies: 6
Views: 3,432
Posted By Tomnl
Hi Vipin Sorry for the delay in replying. I...

Hi Vipin

Sorry for the delay in replying. I have attached a file of the first few lines of the GTF/GFF files I have used.

I should mention: I have managed to get the program to run successfully...
Forum: RNA Sequencing 10-15-2013, 04:12 AM
Replies: 6
Views: 3,432
Posted By Tomnl
Hi Philipp Thanks again for your reply. I...

Hi Philipp

Thanks again for your reply. I tried with a number of different GFF3 files and using a number of different GTF2/GFF3 converters see below... but still no luck.

Would you recommend...
Forum: RNA Sequencing 10-11-2013, 12:45 AM
Replies: 6
Views: 3,432
Posted By Tomnl
Hi philippd, Thank you for the quick...

Hi philippd,

Thank you for the quick response.

I have attached a text file of the output, the first 1000 lines of the GFF3 file and the first 1000 lines of one of the BAM files. I have also...
Forum: Bioinformatics 10-10-2013, 09:05 AM
Replies: 74
Views: 35,472
Posted By Tomnl
Hi all I have found this thread very useful....

Hi all

I have found this thread very useful. Thank you everyone!
(In particular for the comparison paper http://arxiv.org/abs/1304.5952 and post...
Forum: RNA Sequencing 10-10-2013, 08:30 AM
Replies: 6
Views: 3,432
Posted By Tomnl
rDiff - error while getting gene expression

Hi everybody,

I was wondering if anybody could help with an error message I am receiving for the differential isoform analysis software rDiff.
...
Forum: RNA Sequencing 09-24-2013, 01:06 AM
Replies: 0
Views: 2,380
Posted By Tomnl
Changes between Cufflinks/Cuffdiff version 2.0.2 and version 2.1.1

Hey All

I have analysed some RNA-Seq data for a mouse genome with both Cufflinks/Cuffdiff version 2.0 and 2.1 and get quite different results. I understand that there has been a major change for...
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