I have a large fastq file containing NGS sequences. Using prior tools I've been able to narrow down the names of some 2,500 reads which are of interest to me, in OutputFile.txt. In this file there are names of the reads ordered in the following patter:
1123 084b5b69-e819-426f-9ff3-fea4891af330 runid=d20680f0495125cc465d6a96efb49b194cb0777b read=2290 ch=184 start_time=2018-03-27T11:36:09Z 1124 5c621711-9233-40a3-a544-419fe5135d83 runid=d20680f0495125cc465d6a96efb49b194cb0777b read=2382 ch=320 start_time=2018-03-27T11:35:19Z etc...
I'd like to use this OutputFile.txt to extract only the names of the reads and the sequences from the original fastq file into a new filtered fastq file
I have Seqtk installed on windows, running via Command Line.
I believe I could use Seqtk
grep to extract only those 2,500 reads.
I'm having trouble though with the proper command and the flags.
Could you please advise?