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Forum: Bioinformatics 04-27-2017, 06:06 AM
Replies: 2
Views: 1,285
Posted By pbarros
thank you for the input sdriscoll ... maybe I was...

thank you for the input sdriscoll ... maybe I was overthinking this

cheers,
pedro
Forum: Bioinformatics 04-26-2017, 03:19 AM
Replies: 2
Views: 1,285
Posted By pbarros
StringTie - isoforms not overlapping

Hi,
I am using StringTie for transcriptome reconstruction and identification of new isoforms.
While I was exploring the "[file]-transcripts.gtf" output file from stringtie I found something that...
Forum: General 04-05-2014, 09:25 AM
Replies: 2
Views: 1,131
Posted By pbarros
Thanks for the tip GenoMax, it worked!

Thanks for the tip GenoMax, it worked!
Forum: General 04-04-2014, 09:21 AM
Replies: 2
Views: 1,131
Posted By pbarros
Red face Map 6 to 10-mer motifs in reference genome

Dear all,

Recently a coleague asked me if it would be possible to map a specific DNA motif of 8-mer size (transcription factor binding site) in a reference genome (rice), i.e. find all the...
Forum: Bioinformatics 12-06-2012, 08:23 AM
Replies: 4
Views: 2,314
Posted By pbarros
DESeq - High Count Variablity across Samples

Dear Simon,
I am using DESeq in the analysis of RNAseq data, but I'm still doing experiments with the package, to learn how to use it properly for my particular of data... In this analysis I have...
Forum: Bioinformatics 11-23-2012, 07:13 AM
Replies: 11
Views: 14,536
Posted By pbarros
ok! just found the answer for that! :cool: ...

ok!
just found the answer for that! :cool:
never mind
Forum: Bioinformatics 11-22-2012, 09:13 AM
Replies: 11
Views: 14,536
Posted By pbarros
how to convert BLAT output (pslx or maf) to gff, sam, wig to load in browser

Dear all,
I've been trying to use this perl script (psl2sam.pl) to convert a .psl file (from BLAT).
However, this is not generating an output file (.sam)... instead, it just prints (what I think...
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