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BauerLab / ngsane

Analysis Framework for Biological Data from High Throughput Experiments
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bowtie2.sh library tags #28

Closed noncodo closed 10 years ago

noncodo commented 10 years ago

If there is a space in the library tags fields (bowtie2_config.txt), this will cause bowtie2's output to be written to a file name with the text following the space.

Example: Bowtie2_config.txt

# library tags
EXPID="Gene1"
LIBRARY="DNAseq"
PLATFORM="Illumina HiSeq2000"

Will cause a file named HiSeq2000 to be written in the main project folder, and the rest of the task will not pass NGSANE's QC.

Gurado commented 10 years ago

The problem seems to be the way bowtie2 parses its input parameters splitting at every space and ignoring text surrounded by quotes the suggested input would generate, e.g. --sam-rg "PL:Illumina Hiseq2000"

As this is a bowtie2 issue, the recommended workaround is thus to not use any spaces in the library tags.