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Forum: Bioinformatics 12-14-2012, 09:30 AM
Replies: 2
Views: 1,319
Posted By quique_vzquez
Thanks for your answer. Finaly I change the...

Thanks for your answer.
Finaly I change the reads in one of the FASTQ files to their reverse complementary form and I can align them with polarity but I haven't understood yet why it works :S
Forum: Bioinformatics 12-13-2012, 09:38 AM
Replies: 10
Views: 1,783
Posted By quique_vzquez
I separate them from the original .sra file with:...

I separate them from the original .sra file with:
fastq-dump --split-3 originalFile.sra
Forum: Bioinformatics 12-13-2012, 09:17 AM
Replies: 10
Views: 1,783
Posted By quique_vzquez
Are you sure your data isn't paired end? When...

Are you sure your data isn't paired end? When I've got that large reads from Illumina always are paired end.
If it is pair, you must separate your file into two files before align.
Forum: Bioinformatics 12-13-2012, 04:16 AM
Replies: 2
Views: 1,319
Posted By quique_vzquez
Problems with TopHat and Paired End RNASeq

Hi, I'm very new at RNASeq Analysis and I think that I'm doing something wrong.
I've tried to align that data: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS167019.

First I execute...
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