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Forum: Illumina/Solexa 06-15-2011, 10:26 AM
Replies: 58
Views: 52,728
Posted By flobpf
Depends on method

It depends on what method you are using. If you are using Illumina directional sequencing protocol, you get the coding strand sequence. With dUTP, its the template strand. The correct options to use...
Forum: Illumina/Solexa 06-10-2011, 08:16 AM
Replies: 58
Views: 52,728
Posted By flobpf
Talking Resolved

UPDATE June 10, 2011: I contacted Illumina and they were confused too. However, finally they (and people at TopHat and our sequencing center) resolved the issue. The reads that come out of the...
Forum: Illumina/Solexa 03-17-2011, 12:19 PM
Replies: 58
Views: 52,728
Posted By flobpf
Marcowanger, I think you are right. Please see...

Marcowanger, I think you are right. Please see this image attached for an illustrated explanation (and let me know if I'm wrong)...
Forum: Illumina/Solexa 03-17-2011, 04:33 AM
Replies: 58
Views: 52,728
Posted By flobpf
I'm not sure why that is happening. I used tophat...

I'm not sure why that is happening. I used tophat for mapping my reads, am not familiar with BWA.


As far as I understand, TopHat XS:A is not the right FLAG. Strandedness of the read is...
Forum: Illumina/Solexa 03-16-2011, 09:35 AM
Replies: 58
Views: 52,728
Posted By flobpf
HTSeq antisense values

I guess HTSeq is only mapping the reads on the same strand as the annotated feature. Using --stranded=no will (probably) consider all reads mapping to the same locus regardless of the strand, but...
Forum: Illumina/Solexa 02-16-2011, 09:10 AM
Replies: 58
Views: 52,728
Posted By flobpf
Thumbs up Update

I think that the Illumina directional sequencing protocol only does first strand sequencing. So fr-firststrand may be the option to use for TopHat and Cufflinks. Similarly, if you want to find out #...
Forum: Illumina/Solexa 02-07-2011, 01:44 PM
Replies: 58
Views: 52,728
Posted By flobpf
Exclamation Illumina Directional RNA-Seq

Hi,

We recently got single end directional mRNA-Seq data obtained using the new Illumina protocol. I'm trying to map it to the genome using TopHat and Cufflinks. For both programs to understand...
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