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Forum: Illumina/Solexa 04-29-2013, 09:06 AM
Replies: 6
Views: 8,473
Posted By agent99
Poor quality 2nd end from paired-end sequencing on HiSeq

We are seeing very low quality for the first few bases of the 2nd end in paired-end sequencing on the HiSeq. We have data from 6-7 experiments where the library prep and sequencing was conducted at 3...
Forum: Illumina/Solexa 04-29-2013, 07:53 AM
Replies: 11
Views: 8,873
Posted By agent99
Thanks for the response, Hein. That sounds...

Thanks for the response, Hein.

That sounds plausible except that these data are coming from 6-7 different experiments where the libraries were produced and sequenced at 3 different sequencing...
Forum: Illumina/Solexa 04-26-2013, 09:41 AM
Replies: 11
Views: 8,873
Posted By agent99
low quality 2nd read from HiSeq too

We are seeing the same low quality for the first few bases of the 2nd read in paired end sequencing on the HiSeq. We have seen this from multiple sequencing centers and from at least two different...
Forum: Bioinformatics 08-04-2011, 07:40 AM
Replies: 11
Views: 2,755
Posted By agent99
Ah, I just assumed you had short reads because...

Ah, I just assumed you had short reads because you were pasting together such short segments of exons.
Forum: Bioinformatics 08-02-2011, 04:21 PM
Replies: 2
Views: 2,347
Posted By agent99
You could try reducing the segment-length to 1/2...

You could try reducing the segment-length to 1/2 of your read length. I believe that you do not get any mapped splice junctions if your segment-length is greater than 1/2 the read length.
Forum: Bioinformatics 08-02-2011, 04:19 PM
Replies: 11
Views: 2,755
Posted By agent99
I think that if your segment-length is longer...

I think that if your segment-length is longer than 1/2 your read length you won't get any mapped splice junctions.
Forum: RNA Sequencing 01-05-2011, 09:51 AM
Replies: 0
Views: 2,189
Posted By agent99
junctions in tophat

When using TopHat v1.2.0, I am getting 5-fold more junctions identified when I give it an annotation file than when I do not give an annotation file.

12471 junctions - no annotation provided...
Forum: Bioinformatics 12-30-2010, 07:38 PM
Replies: 52
Views: 40,144
Posted By agent99
Thanks for the advice. Apologies for being a...

Thanks for the advice. Apologies for being a little unclear in this post. I had hoped to get transcript level counts, so I was using cufflinks to determine abundance of different isoforms.
Forum: Bioinformatics 12-30-2010, 01:14 PM
Replies: 52
Views: 40,144
Posted By agent99
recovering counts from cufflinks

Did anyone respond to this post?

From the cufflinks output, I tried using the coverage value * (exon length/read length) to get counts, but it doesn't seem to be the right value. My reasoning...
Forum: Bioinformatics 12-22-2010, 06:47 AM
Replies: 11
Views: 6,147
Posted By agent99
You may also need to change MT to chrM for mito...

You may also need to change MT to chrM for mito genes.
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