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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?

weird output

However when I cat into the other pair-end the output seems fine

correct output

Any help/suggestion/solution would be greatly appreciated.

It does seem to be compressed with a missing suffix:

file pair1.fastq
   pair1.fastq: data.
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    $\begingroup$ When I run 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 get pair2.fastq: gzip compressed data, extra field $\endgroup$
    – iichelhadi
    May 13, 2021 at 12:52
  • $\begingroup$ gzip compressed data, extra field is probably produced using bgzip. If it were simple gzip, the extra field part wouldn't be there. $\endgroup$
    – Ram RS
    May 14, 2021 at 18:14

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This indeed looks like some sort of binary file. I have seen bunch of those when people renamed .fastq.gz to .fastq without actually uncompressing them. However, as you say, this is not your case, as file pair1.fastq would identify the file as gzip compressed data.

Looking at possible return values of file comments here, data basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).

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    $\begingroup$ thanks again for the quick response. I was afraid that that might be the case. unfortunately the file came from a collaborator not a public database. I will have to bring that to their attention. $\endgroup$
    – iichelhadi
    May 13, 2021 at 13:06

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