I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I
cat the file I get what seem to me to be binary syntax but not sure?
However when I
cat into the other pair-end the output seems fine
Any help/suggestion/solution would be greatly appreciated.
It does seem to be compressed with a missing suffix:
file pair1.fastq pair1.fastq: data.
file pair1.fastqon the problem fastq file I get the following output:
pair1.fastq: data. When I run it on the other pair-end file which doesn't have any issues I get
pair2.fastq: gzip compressed data, extra field$\endgroup$
gzip compressed data, extra fieldis probably produced using
bgzip. If it were simple
extra fieldpart wouldn't be there. $\endgroup$