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Forum: Bioinformatics 03-01-2011, 12:53 PM
Replies: 0
Views: 2,234
Posted By pcg
Min FPKM Value for Diff Exp

Hi all,

Im wondering do people pre-filter their FPKM values when looking at differential expression. So for instance the levels of expression must be a minimum FPKM > 1 or do people just leave...
Forum: Bioinformatics 02-24-2011, 12:55 PM
Replies: 7
Views: 5,934
Posted By pcg
Thanks Simon for your reply. As you rightly...

Thanks Simon for your reply.

As you rightly point out you do not need a GTF for alignment but if you want to run a cufflinks analysis on the alignment and only want expression for what is...
Forum: Bioinformatics 02-23-2011, 08:34 PM
Replies: 7
Views: 5,934
Posted By pcg
Simon, I presume that if you do exclude the...

Simon,

I presume that if you do exclude the haplotypes in the index then you remove those chromosomes from the GTF annotation file aswell? Right?

So basically if I am understanding correctly...
Forum: Bioinformatics 02-22-2011, 01:47 PM
Replies: 2
Views: 3,854
Posted By pcg
Removal of alternative haplotype chromosomes for expression

A quick question,

Do most people exclude the contigs and haplotype chromosomes from the Human genome (hg19) from their GTF annotation files for chromosome i.e.

GL000191.1
GL000192.1...
Forum: Bioinformatics 01-27-2011, 07:34 AM
Replies: 1
Views: 1,750
Posted By pcg
Differential Expression Analysis Pipeline with Reference

Hi All,

I am wondering what are people's thoughts on the following way to look for DE genes between samples because cuffdiff does not seem to be summing up the FPKM transcripts scores for each...
Forum: 454 Pyrosequencing 08-04-2010, 12:57 PM
Replies: 2
Views: 2,647
Posted By pcg
gsMapper problem

Hi all,

I am using gsMapper v2.3 on a fairly small genome and I really want to see the alignment results but I keep getting the following message.

Error myProject: Unable to launch back-end...
Forum: 454 Pyrosequencing 04-12-2010, 09:15 AM
Replies: 0
Views: 1,917
Posted By pcg
Calculation of Homopolymer errors

Hi All,

Just wondering how do people actually calculate the rate of homopolymer errors in 454 data. For instance If I have a reference sequence and a couple of thousand reads. How would one go...
Forum: Illumina/Solexa 01-07-2010, 02:39 PM
Replies: 1
Views: 2,622
Posted By pcg
Velvet Assemby Reference

Hi All,

Can velvet align to a reference genome and if so how? Also do people have any thoughts on a good hash length. I am trying to align a transcriptome to a reference genome. I have 20M 35bp...
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