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Galaxy Bowtie2 fastq recognition

So Bowtie2 in Galaxy does not recognize my fastq which is output from BBMap Clumpify, has the following message under the input file box: 

Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33

Wondering how I can change the fastq format so it is recognized. Thanks.

galaxy bowtie2 fastq
• 2,388 views • link
written by rbronste rbronste

1 answer

You may have to fastqgroom the file even though it should be in the correct sanger format already. Or use the "pencil" icon to edit the properties --> Datatype tab --> Make sure it is set to fastqsanger/fastqsanger.gz (depending on what format the file is in --> Save.

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written by GenoMax GenoMax

Its odd because I checked it with BBMap:

 bash testformat.sh

and got the following:

sanger  fastq   gz  single-ended    76bp
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written by rbronste rbronste

Odd things happen once you move away from the command line :-)

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written by GenoMax GenoMax

Yes this is generally out of expediency as I am creating several fresh Bowtie2 indexes in the CL.

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written by rbronste rbronste

Why not stick with BBMap suite for downstream analysis? Check the edited answer above if you need to continue with Galaxy.

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written by GenoMax GenoMax

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