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Forum: Bioinformatics 04-23-2010, 06:30 AM
Replies: 10
Views: 9,270
Posted By oliviera
Sorry, The following paper: Nils Homer1,2,...

Sorry,
The following paper:
Nils Homer1,2, Barry Merriman2*, Stanley F. Nelson2, Plos one 2009
compare bfast and bowtie. Forget my last question...
I should have read the paper befor sending the...
Forum: Bioinformatics 04-23-2010, 06:21 AM
Replies: 10
Views: 9,270
Posted By oliviera
Hi Poisson, Yes you are right. I have only...

Hi Poisson,

Yes you are right. I have only 36bp and single end reads and tophat is optimised for paired end. But still the authors claims that it could be used. To which extend I do not know... ...
Forum: Bioinformatics 04-23-2010, 04:30 AM
Replies: 10
Views: 9,270
Posted By oliviera
I do the mapping against the zebrafish genome,...

I do the mapping against the zebrafish genome, and then use the annotated USCS genome for the localisation of the exon.
I agree with you that blat should not be able to map the exon-exon reads. The...
Forum: Bioinformatics 04-23-2010, 03:41 AM
Replies: 10
Views: 9,270
Posted By oliviera
Thanx for your fast reply joa, I fear like you...

Thanx for your fast reply joa,
I fear like you that using blat will make the whole downstream analysis difficult.
I have however tested already blat on a subset of my data and what I get is similar...
Forum: Bioinformatics 04-23-2010, 02:34 AM
Replies: 10
Views: 9,270
Posted By oliviera
Smile Blat vs bowtie/tophat on Rnaseq data

Dear all,
This is my first thread here, so hello everyone!
:)
I am new in the field, so I hope my questions are not too trivial and could interest some of you.

We have RNAseq data 36bp single...
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