Hi guys =) I'm sorry if this is a repeat but I haven't been able to find an answer using the search field or google.
I am trying to edit a fastq file that has a corrupt line. The read in question is VH00362:5:AAAV5KTHV:1:1210:64850:6869 where the read is just a massive repeat – not the expected 110bp. I am trying to remove two lines from this file and asking around I've been told to use
sed as in
gzip -c file.fastq.gz | sed "45500973,45500974d" > new.fastq.gz
but when I run
wc -l to check the number of lines the results are incoherent, as if it has deleted much more than the two lines I asked. Another issue that I'm seeing with this file is that every time I run
gzip I get a
invalid compressed data--format violated error, which tells me the file is corrupted but I'm doing my best to salvage whatever I can from the file as it is an irreplaceable sample.
Is there another way to simply delete these two lines? Any tool or command you could recommend? Any help is deeply appreciated.
gzip -k file.fastq.gzreport an error? If so, I would first try to
gunzipthe file, or
zcat file.fastq.gz > file.fastqand then operate on the decompressed one. I am not sure, but I suspect that a corrupted archive might not
catas expected and I would feel safer getting as much of the file decompressed as I can first. I am not even sure you will get anything, please try and report back. $\endgroup$