I have copies of the same `fastq file` (let's call it `samp1_R1.fastq.gz`) in two different locations (e.g., `/foo/samp1_R1.fastq.gz` and  `/bar/samp1_R1.fastq.gz`). These files are supposed to be identical (the one at `/foo` is a "working copy" while the one at `/bar` is a backup).

I happened to generate MD5 checksums from both these files today, and to my surprise, the hashes are different:

    $ md5sum /foo/samp1_R1.fastq.gz
    13a75f5e319fa772faa85beb04317718 /foo/samp1_R1.fastq.gz
    
    $ md5sum /bar/samp1_R1.fastq.gz
    e7a4f3c293361fa569a192f8a26a141d /bar/samp1_R1.fastq.gz


Does this truly mean that the files are now different? I cannot think of anything that could have modified one of these files (the "working copy" was only ever used as an input to standard RNA-seq tools). Could the mere act of uncompressing (and recompressing) the file update the hash like that? (That's the only thing I can recall doing to the file itself.)

Now I'm also wondering whether I should rerun analyses that were based off of this file.

Your inputs would be appreciated.
different compression level ? names changed ?

check with:

    gunzip -c /foo/samp1_R1.fastq.gz | md5sum

    gunzip -c /bar/samp1_R1.fastq.gz | md5sum

or/and

    paste <( gunzip -c /foo/samp1_R1.fastq.gz)  <( gunzip -c /bar/samp1_R1.fastq.gz)  | awk -F '\t'  '($1!=$2)'