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Forum: RNA Sequencing 04-24-2013, 09:37 PM
Replies: 5
Views: 3,072
Posted By tgenahmet
same problem here. Any fixes, anyone?

same problem here. Any fixes, anyone?
Forum: Bioinformatics 04-13-2012, 11:57 AM
Replies: 2
Views: 5,182
Posted By tgenahmet
tophat2 problem: No such file: left_kept_reads.m2g_um.candidates_and_unspl.bam

I'm running into this problem while trying to get tophat2 to work. I'm running this on the test data that came with the software.

I did get an accepted_hits.bam but it only contains the header.
Forum: Bioinformatics 01-03-2012, 12:29 PM
Replies: 7
Views: 5,199
Posted By tgenahmet
I'm also running into this issue - but it seems...

I'm also running into this issue - but it seems like a different stage:

Any ideas?
Forum: Bioinformatics 12-26-2011, 09:02 AM
Replies: 4
Views: 8,017
Posted By tgenahmet
bowtie index problem (bowtie-build and then bowtie-inspect)

I used bowtie-build to build an index:
~/bin/bowtie/bowtie-build human_g1k_v37.fa human_g1k_v37
It seemed to complete just fine:

Created these files:

But when I run bowtie-inspect:...
Forum: Illumina/Solexa 12-08-2011, 07:36 AM
Replies: 8
Views: 6,303
Posted By tgenahmet

I ran into the same problem when I used --static while running configure. Removed --static and now it is past that step.
Forum: Bioinformatics 10-27-2011, 09:47 AM
Replies: 3
Views: 15,758
Posted By tgenahmet
insert PG and CL tags into BAM header with BWA

What do you recommend I use to insert full command line into the BAM header created with BWA. BWA already creates this:

@PG ID:bwa PN:bwa VN:0.5.9-r16

But I'd like to capture the whole process...
Forum: Bioinformatics 07-05-2011, 09:42 AM
Replies: 10
Views: 7,944
Posted By tgenahmet
We're also having very similar issues. Our...

We're also having very similar issues. Our clusters gives us 96 hours to complete our jobs but sometimes we hit this wall time. Any tips to improve speed with cufflinks are highly appreciated.
Forum: Bioinformatics 10-15-2009, 01:37 PM
Replies: 1
Views: 4,376
Posted By tgenahmet
using BWA to align SOLiD fastq files from 1000 Genomes

Hi All,

I've been playing with BWA to align some color space data from 1000 Genomes. So far all my alignments are TNNNNNNNNNNNNNNNN's.

I'm trying to figure out the correct procedure for using...
Forum: Bioinformatics 06-03-2009, 01:09 PM
Replies: 3
Views: 4,817
Posted By tgenahmet
We were running it with 36bp reads.

We were running it with 36bp reads.
Forum: Bioinformatics 05-29-2009, 03:10 PM
Replies: 3
Views: 4,817
Posted By tgenahmet
BWA memory issues

We're trying to use BWA with paired end reads (bwa sampe with default settings) and running into memory problems when aligning to whole human genome. It maxes out our memory on a machine with 24GB of...
Forum: Bioinformatics 05-05-2009, 12:07 PM
Replies: 8
Views: 15,554
Posted By tgenahmet
convert qseq to fastq that maq or bwa can use

Hi all,

I'm new here.

I have the Illumina pipeline 1.3 installed. I'd like to use BWA for aligning. I need to get from qseq files to phred fastq files.

Is there a tool that already exists...
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