Forum: Bioinformatics
03-30-2016, 07:51 PM
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Replies: 1
Views: 1,777
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:
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Forum: Bioinformatics
03-02-2016, 11:06 AM
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Replies: 0
Views: 2,389
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...
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Forum: Bioinformatics
11-14-2015, 10:40 AM
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Replies: 2
Views: 2,717
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Forum: Bioinformatics
11-13-2015, 01:31 PM
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Replies: 2
Views: 2,717
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...
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Forum: Bioinformatics
09-23-2015, 12:00 PM
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Replies: 0
Views: 1,800
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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