Trim Galore! can't find fastq files

1

Dear all,

i have cutadapt raw output files and want to run cutadapt to trim nextera transposase sequences. Trim galore can’t find any files neither my original fastq.gz files. Could you please help me?

Thanks in advance,

Best
Bernhard

2

Hi @Bernhard,
most likely your files have ‘fastq.gz’ datatype in Galaxy, eg format: fastq.gz. Cutadapt recognizes this datatype, while Trim Galore works with datatype like fastqsanger.gz. Similar topic discussed on the forum, eg Unicycler failed - "reads unavailable" -- Inputs not recognized due to an incompatible datatype assignment - #3 by vanina.guernier

Kind regards,
Igor

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