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Search: Posts Made By: ccstaats
Forum: Bioinformatics 04-12-2013, 03:09 PM
Replies: 4
Views: 2,832
Posted By ccstaats
Hi, leifive. Sorry for the long time to answer....

Hi, leifive.
Sorry for the long time to answer.
In fact, I used velvetg and velveth
I've got some good results results. Found some genes that should be there. They are not, as the genome is not...
Forum: Bioinformatics 01-22-2013, 12:41 PM
Replies: 0
Views: 803
Posted By ccstaats
Read counts in SOAPdenovotrans output

Hello all
I am working with a few libraries of small RNAs (20 - 200 nt) from yeast.
So, I want to do a functional characterization of the RNAs in such libraries.
For this, I am building contigs...
Forum: Bioinformatics 01-22-2013, 11:31 AM
Replies: 4
Views: 2,479
Posted By ccstaats
Dear all. I Just realized that the process is...

Dear all.
I Just realized that the process is quite long. The data analysis (4 Gb of fasta files) runned in 3 hours in a I5 processor with 8gb RAM.
Thank you all.
Charley
Forum: Bioinformatics 01-21-2013, 06:34 AM
Replies: 4
Views: 2,479
Posted By ccstaats
Randfol in miRDeep2

Hello all,
I am trying to get miRDeep 2 to work with my data.
Everything goes fine with mapping, collapsing, etc.
When I try to run the mirDeep2.pl using the script
perl mirDeep2.pl...
Forum: Bioinformatics 02-22-2012, 06:13 AM
Replies: 4
Views: 2,832
Posted By ccstaats
Thank you Works nice. Charley

Thank you
Works nice.
Charley
Forum: Bioinformatics 02-22-2012, 03:41 AM
Replies: 4
Views: 2,832
Posted By ccstaats
de novo assembly using unmapped reads from tophat

Hello
There is a way to use the unmapped reads from tophat 1.4.1 to build a de novo assembly?
I ve been looking for programs to do this and I found SOAPdenovo.
But first, I tried to take a look at...
Forum: Bioinformatics 02-20-2012, 12:14 PM
Replies: 0
Views: 849
Posted By ccstaats
2 trancripts identified by cufflinks with the same sequence

So, I've run tophat, cufflinks and cuffdiff from my rna seq.
Using the Broad institute provided gtf files, the programs mapped finely and I observed that some new transcripts were discovered. ...
Forum: Bioinformatics 02-02-2012, 05:28 AM
Replies: 0
Views: 2,063
Posted By ccstaats
cuffmerge problems

Hello
I'm founding some problems with cuffmerge
I've a fasta file of 27 supercontigs from broad institute, which I edited to this format
>Supercontig_1.1

I've downloaded also the gtf file from...
Forum: Bioinformatics 02-01-2012, 07:36 AM
Replies: 2
Views: 1,508
Posted By ccstaats
Thank you. It helps a lot Charley

Thank you.
It helps a lot
Charley
Forum: Bioinformatics 01-31-2012, 10:51 AM
Replies: 2
Views: 1,779
Posted By ccstaats
Hello jbrwn Thank you for your answer I think...

Hello jbrwn
Thank you for your answer
I think I've found a way to escape away from this problem
I was only considering the transcript fasta file from the Broad Institute.
Know, I got the whole...
Forum: Bioinformatics 01-31-2012, 10:11 AM
Replies: 2
Views: 1,508
Posted By ccstaats
Graphical visualization of GFT files

Hello all
Using tophat, cufflinks and cuffmerge, I found lots of new genes.
I would like to graphically visualize the information of the GFT files in the genome sequence (something like artemis)....
Forum: Bioinformatics 01-31-2012, 04:35 AM
Replies: 2
Views: 1,779
Posted By ccstaats
TopHat - Cufflinks problems in a transcript multifasta file whitout coordinates

Hello all
I'm new to rnaseq analysis, so I wonder if you guys can help me with some issues.
So, I'm trying to evaluate differential expression from the WT and a mutant strain of a yeast, whose...
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