Header change in NCBI SRR files
Hi all
I have downloaded some SRR and ERR fastq files for my research purpose and I would like to change the headers in SRR files. It would be helpful if any one suggest some possible ways to change it.
Example header seq present in fastq file
@SRR1969129.2 2 length=150
@SRR1969129.3 3 length=150
I would like to change it like:
@SRR1969129-2-2
@SRR1969129-3-3
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Anda •
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genomics_buddy •
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genomics_buddy •
1 answer
you can try this sed:
sed -i "s/ length=150//g ; s/ /-/g ; s/\./-/g" YOUR_FASTQ_FILE
explanation: first, space and the following length=150 is removed then the remaining space is replaced with "-" and finally the "." is replaced with "-". all happens in place due to the "sed -i"
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