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Forum: RNA Sequencing

04-24-2013, 09:37 PM

Replies: 5

tophat-fusion-post: KeyError: 'score'

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

tophat2 problem: No such file: left_kept_reads.m2g_um.candidates_and_unspl.bam

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

Tophat Fusion error with mRNAseq data

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

bowtie index problem (bowtie-build and then bowtie-inspect)

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

HELP! CASAVA_v1.7.0 Install error:pthread library not found

Views: 6,303

Posted By tgenahmet

--static

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

insert PG and CL tags into BAM header with BWA

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

Cufflinks Runtime

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

using BWA to align SOLiD fastq files from 1000 Genomes

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

BWA memory issues

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

BWA memory issues

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

convert qseq to fastq that maq or bwa can use

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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