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Forum: General 11-24-2011, 02:37 AM
Replies: 0
Views: 1,687
Posted By sohnic
[BLASTP] where are some hits ?

Hello,
We have a problem with blastp (we've tried blastall, blast++, standalone or web server).
We have a small database of proteins domains (between 30-100 aa, about 700 domains) and want to test...
Forum: Bioinformatics 06-09-2011, 06:54 AM
Replies: 3
Views: 4,396
Posted By sohnic
cufflinks : analysis comparison with and without a gtf reference file

Hi,
I have many questions about cufflinks output. Here one of them :
First I've used tophat to map my RNAseq (100pb) to obtain a accepted_hits.bam file.
Then I've used cufflinks in two ways :
-...
Forum: Bioinformatics 03-25-2011, 02:30 PM
Replies: 4
Views: 3,932
Posted By sohnic
Hi, The sequencing compagny confirms the use of...

Hi,
The sequencing compagny confirms the use of the solexa1.3-quals option.
And, fastQC, that seems to be a really good application says the same thing (solexa>1.3).
Many thanks !

S.
Forum: Bioinformatics 03-25-2011, 07:51 AM
Replies: 4
Views: 3,932
Posted By sohnic
Hi, Thanks a lot for those very interesting...

Hi,
Thanks a lot for those very interesting informations.
So, I thing I have to use the solexa1.3-quals option in my case.
To be sure, I've asked the sequencing society. I'm waiting their...
Forum: Bioinformatics 03-24-2011, 09:15 AM
Replies: 4
Views: 3,932
Posted By sohnic
tophat - solexa options

Hi,
Does anyone known where to find information about the following tophat options:
--solexa-quals
--solexa1.3-quals

I have to align fastq reads (100 nt) issued from a “Hi-Seq 2000” on a...
Forum: Introductions 03-22-2011, 10:02 AM
Replies: 0
Views: 822
Posted By sohnic
Hello

Hello,
I work in a french academic lab, in a bioinformatic service.
Our job consists to help research teams to explore and analyse their sequence data (genomics, transcriptomics, proteomics of...
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