Galaxy Bowtie2 fastq recognition

Question

[rbronste]

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.

Answer 1

[GenoMax]

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.

[rbronste]

Its odd because I checked it with BBMap:

 bash testformat.sh

and got the following:

sanger  fastq   gz  single-ended    76bp

[GenoMax]

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

[rbronste]

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

[GenoMax]

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