I set up a local installation of Galaxy and have been trying to
reproduce inside it what I had previously accomplished with command-line
scripts. One of the tools that I'm using is BWA, so I installed the "Map with
BWA Illumina" tool from the tool shed. So far so good. However, when performing
alignments at the command-line, I was able to directly input fastq.gz files
onto BWA, which doesn`t seem to be possible inside Galaxy.
Besides saving a lot of storage space, working with gzipped
fastq files turned out to give me faster results too, so it's a "must have"
feature for me. When I try to create a BWA task, the form complains that there
isn`t any compatible file in my history. If I try to see the files contents,
there's an error message complaining about their encoding. If I gunzip the
files, everything works fine.
Am I falling into any beginner's dumbness?
Thanks in advance.
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