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Forum: Bioinformatics 10-03-2014, 01:56 PM
Replies: 5
Views: 1,544
Posted By Peppe
Thanks amitm, I did and it worked fine. Now I...

Thanks amitm,
I did and it worked fine. Now I have gene names for all my transcripts. By change do you know how to have also Saccharomyces gene descriptions? This would be ideal.

I think in...
Forum: Bioinformatics 10-03-2014, 09:26 AM
Replies: 5
Views: 1,544
Posted By Peppe
Thanks amitm. In the way you said should I do...

Thanks amitm.
In the way you said should I do the conversion manually? Or is there an informatic way?
Best.
Forum: Bioinformatics 10-03-2014, 08:22 AM
Replies: 5
Views: 1,544
Posted By Peppe
BLAST comparison between two sets of sequences

Hello everyone,
I have a set of sequences generated with Trinity and I want to compare them with S. cerevisiae. I have downloaded the S. cerevisiae protein set from the SGD. Since S. cerevisiae is a...
Forum: Introductions 10-03-2014, 08:03 AM
Replies: 1
Views: 1,230
Posted By Peppe
BLAST comparison between two sets of sequences

Hello everyone,
I have a set of sequences generated with Trinity and I want to compare them with S. cerevisiae. I have downloaded the S. cerevisiae protein set from the SGD. Since S. cerevisiae is a...
Forum: Introductions 11-29-2012, 10:35 AM
Replies: 4
Views: 1,982
Posted By Peppe
Thanks hjtripp

Thanks hjtripp
Forum: RNA Sequencing 11-28-2012, 03:36 PM
Replies: 27
Views: 58,173
Posted By Peppe
Thanks Jeremy. I will use the Galaxy user...

Thanks Jeremy.
I will use the Galaxy user community: http://user.list.galaxyproject.org/
Forum: Introductions 11-26-2012, 04:42 PM
Replies: 4
Views: 1,982
Posted By Peppe
Hello Jim, I see you are at the JGI and I...

Hello Jim,
I see you are at the JGI and I though to ask you an advice/question. I am performing RNAseq analysis using a yeast whose genome sequence is available on the JGI website. I downloaded both...
Forum: RNA Sequencing 11-26-2012, 04:30 PM
Replies: 27
Views: 58,173
Posted By Peppe
As you guys can see in the previous messages, I...

As you guys can see in the previous messages, I am new in this field. I am using the public Galaxy server, and for the first time I run sample with TopHat-Cufflink-Cuffcompare-Cuffdiff. Can anyone...
Forum: RNA Sequencing 11-19-2012, 09:34 PM
Replies: 27
Views: 58,173
Posted By Peppe
Hello, I tried to run cufflinks after TopHat...

Hello,
I tried to run cufflinks after TopHat mapping and as a genome reference annotation it requires a file in gtf format. I downloaded the genome annotation from the JGI website (I am working with...
Forum: RNA Sequencing 11-19-2012, 08:32 PM
Replies: 27
Views: 58,173
Posted By Peppe
Thanks jgoecks, Yes, I am using the public...

Thanks jgoecks,
Yes, I am using the public Galaxy server.
As you said the job took a while to start, but after that it was quick enough. Now there is an update of the server so I have to wait....
Forum: RNA Sequencing 11-18-2012, 11:22 AM
Replies: 27
Views: 58,173
Posted By Peppe
Hi all, I am new in the forum and also in the...

Hi all,
I am new in the forum and also in the RNA seq analysis field.
I just a got the results of my RNA sequencing and I am trying to map my reads using tophat on galaxy. I am working with...
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