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Forum: Bioinformatics 03-30-2016, 07:51 PM
Replies: 1
Views: 1,777
Posted By jpmatteson
fastq-dump errors

I'm getting two errors on certain fastq-dump jobs. I am submitting jobs to HTCondor using a dag file to manage downloads. I am queuing multiple jobs and sometimes I get the following errors:
...
Forum: Bioinformatics 03-02-2016, 11:06 AM
Replies: 0
Views: 2,389
Posted By jpmatteson
Header missing from .bwt -> .sam conversion

I am using bowtie and have been outputting .bwt files but now need to convert those files to .sam format. I know bowtie has a .sam output option (-S) which I am now using, however I need to convert...
Forum: Bioinformatics 11-14-2015, 10:40 AM
Replies: 2
Views: 2,717
Posted By jpmatteson
Thanks, that helps a lot.

Thanks, that helps a lot.
Forum: Bioinformatics 11-13-2015, 01:31 PM
Replies: 2
Views: 2,717
Posted By jpmatteson
Bowtie output and reference genome question

Hello, a quick question for anybody familiar with bowtie. In my reference genome files, which have names like SVID_XXX, the first line of text, before the actual sequence data is a line like...
Forum: Bioinformatics 09-23-2015, 12:00 PM
Replies: 0
Views: 1,800
Posted By jpmatteson
Bowtie output file help

I'm using bowtie to do alignments, the index is made from 96 bacterial genomes, some genomes are incomplete and composed of many contigs. The fasta index files for the contigs are broken up by lines...
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