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Forum: Bioinformatics 07-29-2014, 12:45 PM
Replies: 0
Views: 1,342
Posted By AnneBiton
STAR: Alignment reported with less matches than parameter --outFilterMatchNmin

Hello,

I am using STAR_2.3.0e.Linux_x86_64 to align only the first 25b of my paired-end reads, with the parameters:
--outFilterMatchNmin 40

--clip5pNbases 4 (there 4 random pairs before the...
Forum: Bioinformatics 06-05-2013, 03:40 PM
Replies: 1
Views: 1,422
Posted By AnneBiton
Convert Sam file with incorrect fields to Fastq using HTSeq

Hello,

I am working with BAM/SAM files generated by MapSplice on (human) RNA-seq paired-end reads from Illumina HiSeq. I want to convert them into fastq in order to realign them (I don't have...
Forum: Bioinformatics 08-24-2012, 12:34 AM
Replies: 5
Views: 3,289
Posted By AnneBiton
Removing the /1 and /2 worked for this problem,...

Removing the /1 and /2 worked for this problem, thanks! The MapSplice alignments I have seem to contain a lot of incorrect SAM fields...
Forum: Bioinformatics 08-22-2012, 02:50 PM
Replies: 5
Views: 3,289
Posted By AnneBiton
Many thanks for your replies! I temporarily...

Many thanks for your replies!
I temporarily discarded these fusion reads and I will have a look at the script to modify their flags.

After having discarded them, I have HTSeq warnings saying that...
Forum: Bioinformatics 08-20-2012, 05:25 PM
Replies: 5
Views: 3,289
Posted By AnneBiton
Error using HTSeq on Mapsplice alignments

Hello,

I am trying to use HTSeq-0.5.3p9 with python2.7 to get the counts from genomic regions defined in a gff file.
My data are BAM files generated by MapSplice on (human) RNA-seq paired-end...
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