Does fastx_toolkit accept *fastq.gz file as input file? Or does it have to be fastq/a file?
I get the following error message when i try
fastx_clipper -Q33 -z -a GATC -i my.fastq.gz -o my_adapRem.fastq
fastx_clipper: input file (my.fastq.gz) has unknown file format (not FASTA or FASTQ), first character = (31)
is this because of zipped input data or am i missing something else?
2 answers
jake9115 may have answered your question literally (no fastx-toolkit doesn't read .gz), but you should know that they DO take STDIN. Thus, since you're on a command line (or in a script), make a pipe:
gunzip -c my.fastq.gz | fastx_clipper -Q33 -z -a GATC -o my_adapRem.fastq
FASTX-Toolkit only can output files in compressed format, not use them as input. According to the documentation:
Some tools can compress the output with GZIP (-z).
Only in one reported case can the input be gzipped:
fasta_clipping_histogram.pl help page includes this:
INPUT_FILE.FA = input file (in FASTA format, can be GZIPped)
Hope that helps!
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