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Search: Posts Made By: Anna Esteve
Forum: Bioinformatics 09-30-2010, 12:24 PM
Replies: 18
Views: 5,033
Posted By Anna Esteve
I run Cufflinks v0.9.0 with default options but...

I run Cufflinks v0.9.0 with default options but setting -N and -r. When I use the -G option (reference annotation gtf) I have some transcripts in the transcripts.gtf output that are no present in the...
Forum: Bioinformatics 08-23-2010, 02:14 AM
Replies: 38
Views: 21,402
Posted By Anna Esteve
total mapped fragments RNA-seq

I am interested in having read counts for RNA-seq differential expression analysis. Does anybody know how to count the total number of fragments mapped if my Sam file (from Tophat) have a mixture of...
Forum: Bioinformatics 08-16-2010, 04:09 AM
Replies: 191
Views: 77,423
Posted By Anna Esteve
I am having the same problem as you, when i run...

I am having the same problem as you, when i run HTseq-count I have warnings about improper mate pairs. Tophat sam output contains improper mate pairs (the mate is unmapped) as well as proper pairs....
Forum: Bioinformatics 07-27-2010, 03:30 AM
Replies: 2
Views: 1,365
Posted By Anna Esteve
Cufflinks reports that doesn't support NH, CC and...

Cufflinks reports that doesn't support NH, CC and CP attributes. So I had to delete all this attributes from my Sam file and now I think is working fine.
Forum: Bioinformatics 07-26-2010, 03:02 AM
Replies: 2
Views: 1,365
Posted By Anna Esteve
Cufflinks, attribute not supported

Hi,
I run Cufflinks with sam input (from Tophat) and I got this error message thousands of times:
'NH attribute not supported'
Does anyone know how to solve this problem?
Thanks in advance.
Forum: Bioinformatics 06-07-2010, 08:40 AM
Replies: 1
Views: 1,891
Posted By Anna Esteve
soap2 and fastq

Hi, I would like to know which of these three fastq formats is suitable for soap2:

Sanger standard
    fastq-sanger 33126 33 PHRED 0 to 93
Solexa/early Illumina ...
Forum: Bioinformatics 05-26-2010, 08:11 AM
Replies: 0
Views: 1,563
Posted By Anna Esteve
soapsnp error

Hi,
I am using soapsnp and I've got this message error:

Reading Chromosome and dbSNP information Done.
Correction Matrix Done!
Processing X
Processing 1
Broken ofstream after writting...
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