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Forum: Bioinformatics 03-20-2012, 09:29 PM
Replies: 4
Views: 2,495
Posted By ngs_agd
Can you please elaborate on this? What was the...

Can you please elaborate on this? What was the organism, how much data did you provide, the platform on which the data was generated, how long it took to complete the assembly etc. Greatly appreicate...
Forum: Bioinformatics 03-20-2012, 06:01 AM
Replies: 4
Views: 2,495
Posted By ngs_agd
CLC genomics server for assembling large genomes

Has anybody tried using CLCBio Genomics server for assembling large genomes (Panda, Human etc)?

We have interest in assembling large genomes with small amount of RAM. Tried using CLCBio server...
Forum: Bioinformatics 05-10-2011, 12:59 AM
Replies: 26
Views: 14,634
Posted By ngs_agd
Hi Honey, Sorry if I am not being clear. This...

Hi Honey,
Sorry if I am not being clear. This is what I have done so far and I am struggling to make some sense of the information I am getting:
1. I have 2 .bam files (1 control and 1 disease). I...
Forum: Bioinformatics 05-09-2011, 11:05 PM
Replies: 26
Views: 14,634
Posted By ngs_agd
Sorry, in my previous thread I had asked whether...

Sorry, in my previous thread I had asked whether the cuffcompare file needs to be edited. I just looked at a cuffcompare file, it seems to have only annotation information and no FPKM values. So, how...
Forum: Bioinformatics 05-09-2011, 10:26 PM
Replies: 26
Views: 14,634
Posted By ngs_agd
Does this mean that I will have to download the...

Does this mean that I will have to download the cuffcompare file, edit it, upload it on galaxy and then run cuffdiff on this gtf file? Thanks for your help!
Forum: Bioinformatics 05-09-2011, 10:21 PM
Replies: 1
Views: 1,863
Posted By ngs_agd
How Cuffcompare works?

I have used Galaxy to do RNASeq analysis. I don't quite understand the Cuffcompare part.
When running cuffcompare (considering that I am using Cuffdiff afterwards), do I have to provide the 2...
Forum: Bioinformatics 02-22-2011, 09:31 PM
Replies: 3
Views: 1,683
Posted By ngs_agd
duplicate reads in enriched samples

Hi all,
I have some RNAseq data (enriched and non-enriched) generated on Illumina. I am seeing a lot of duplicate reads (as well as much higher read depth) in the enriched dataset. Does enrichment...
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