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Search: Posts Made By: mmanrique
Forum: Bioinformatics 09-11-2013, 04:17 AM
Replies: 2
Views: 1,354
Posted By mmanrique
Hey, take a look at this thread ...

Hey, take a look at this thread

http://seqanswers.com/forums/showthread.php?p=98872

is this what you wanted to do?
Forum: Bioinformatics 08-01-2012, 08:49 AM
Replies: 6
Views: 11,216
Posted By mmanrique
Hi, we had the same problem and tried the...

Hi,

we had the same problem and tried the new Cufflinks version 2.0.2 and it seems the values from Cufflinks and Cuffdiff are the same (have to check it more carefully)

these are the commands I...
Forum: Bioinformatics 01-31-2012, 08:57 AM
Replies: 1
Views: 1,298
Posted By mmanrique
Why don't you try using the BAM file instead of...

Why don't you try using the BAM file instead of the SAM one?
Forum: Bioinformatics 11-28-2011, 01:15 AM
Replies: 3
Views: 4,596
Posted By mmanrique
you can get it here ...

you can get it here
http://www.illumina.com/support/sequencing/sequencing_kits/truseq_exome_enrichment_kit/downloads.ilmn
Forum: Bioinformatics 05-28-2010, 01:52 AM
Replies: 4
Views: 2,026
Posted By mmanrique
Hi pr0t3us, thanks very much for your...

Hi pr0t3us,

thanks very much for your reply. It's good to know it's a bug

Marina
Forum: Bioinformatics 05-27-2010, 02:11 AM
Replies: 4
Views: 2,026
Posted By mmanrique
Error in contigs length in 454AllContigs.fna 454 Output file

Hi there,

Checking out the 454 output file 454AllContigs.fna I've found out some errors in contig length. There are some cases where the contig length written in the fasta header is clearly...
Forum: Bioinformatics 02-12-2010, 03:13 PM
Replies: 10
Views: 7,010
Posted By mmanrique
Thanks a lot for the answers :)

Thanks a lot for the answers :)
Forum: Bioinformatics 02-09-2010, 03:53 AM
Replies: 10
Views: 7,010
Posted By mmanrique
Hi! it's good to know that DEGseq works...

Hi!

it's good to know that DEGseq works fine. I would like to know if it's necessary to have several sample replicates to use this package,

thanks!

marina
Forum: Bioinformatics 02-08-2010, 02:39 AM
Replies: 10
Views: 7,010
Posted By mmanrique
DEGseq or edgeR

Hi,

I need to analyze differentially expressed genes between samples from two tissues. I was thinking about using DEGseq or edgeR packages,

any of you have tried these packages?

thanks!
...
Forum: Bioinformatics 02-04-2010, 07:26 AM
Replies: 28
Views: 13,865
Posted By mmanrique
I'm looking forward trying Crossbow! It's...

I'm looking forward trying Crossbow!

It's satisfying finding other guys using and promoting cloud computing for bioinformatics analyses :)

Congratulations!
Forum: Service Providers 01-21-2010, 06:38 AM
Replies: 162
Views: 158,310
Posted By mmanrique
Dear ECO, first of all thanks very much for...

Dear ECO,

first of all thanks very much for the list. Really useful.

I have seen IT companies in the list so I would like to present Era7 Bioinformatics. It would be
Era7 Bioinformatics...
Forum: Bioinformatics 01-05-2010, 09:02 AM
Replies: 15
Views: 4,627
Posted By mmanrique
Hi Arthur, have you tried getting .SAM files...

Hi Arthur,

have you tried getting .SAM files using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) instead of Tophat? I think it would work although I haven't tried it yet.
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