Can renaming, copying, or moving the fastq files, bam/sam file, or reference genome file corrupts it. I am facing this issue of file corruption. What can be the cause and what I can do in order to fix the issue? Or I need to get the files again?
Doing anything (or even nothing) to a file can corrupt it if you have hardware or network problems. If there are no network or hardware problems (and no stray solar rays) then renaming/copying/moving any file shouldn't corrupt it.
Thank you for your reply. Is there any technique to know whether it is hardware, network, or stray solar rays problem?
I have used GATK and PICARD to validate SAM/BAM/ files.
If you are making copies of a file, particularly if the copy is going to be downloaded off a server, then using md5sum will produce a hash (string of characters) that are unique to the file, and can be matched with the copy.
moving or copying large file in linux has a risk that files may get corrupted. Its is recommended to use Rsync which ensure data integrity in linux.
Another option if it's a very large file you don't want to move or duplicate, is to create soft/symbolic links (shortcuts) to the file, and then to operate on the shortcuts instead.
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Your question is lacking any detail. Please read and follow How To Ask Good Questions On Technical And Scientific Forums. What files are you working with, and what is the evidence for corruption?