Hi friends,
Got a small problem because of my fastq file which is wrong. So I wanted to correct lines manually.
For example I got these lines in my test.fasq file:
@HWI-ST1194:55:C11P5ACXX:4:2316:21380:54479/2
ATAATCTTCCCCAAGCATGGAACAAATACTCTCTTTAGTGGACTTGCATAACCTACAAAAAAACCTTCGTTAACTTT
+
@#1==DDAFFFD=EFFB1CGEEFECFFGIIIIIEGII?DFECEEFDEAFEEII;?A1([M::main_bam2fq] discarded 8840174
Wanted to replace the last line by a real quality :
@@BFFFFFHFFHBFHHIBEE>GIGHEHG+CG3CFFGGIIDBDGGGFDFGEDFHGCCGHEFHE;7@DEDFDACCECDC>
So my command line:
sed '4 s/@#1==DDAFFFD=EFFB1CGEEFECFFGIIIIIEGII?DFECEEFDEAFEEII;?A1([M::main_bam2fq] discarded 8840174/*@@BFFFFFHFFHBFHHIBEE>GIGHEHG+CG3CFFGGIIDBDGGGFDFGEDFHGCCGHEFHE;7@DEDFDACCECDC>*/g' test1
What's wrong ? Or can I proceed with perl maybe?
Thanks
please, format your post. It's hard to see what's wrong.
Hi Pierre,
I've put it here: