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.fastq
on 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 getpair2.fastq: gzip compressed data, extra field
$\endgroup$gzip compressed data, extra field
is probably produced usingbgzip
. If it were simplegzip
, theextra field
part wouldn't be there. $\endgroup$