I have a FASTQ file:
@NS500455:80:HG7TNBGXB:1:11101:17723:1055 1:N:0:ATCACG
ACTTANGTGTATGTAAACTTCCGACTTCAACTGTATAGGGATCCNAGCTCCAATTCGCCCTATAGTGAGTCGTAT
+
/AAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
@NS500455:80:HG7TNBGXB:1:11101:8821:1057 1:N:0:ATCACG
ACTTANGTGATGTAAACTTCCGACTTCAACTGTATAATAAATATCTAGATCGGAAGAGCACACGTCCGAACTCCA
I want to remove the string ACTTAAGTGTATGTAAACTTCCGACTTCAACTG from it while retaining the sequences starting from TA onwards.
I wrote grep "ACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA" SRR_1.fastq | sed "s/ACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA/TA/g"
, but it removes the headers of the FASTQ file as well.
The desired output would be
@NS500455:80:HG7TNBGXB:1:11101:17723:1055 1:N:0:ATCACG
TATAGGGATCCNAGCTCCAATTCGCCCTATAGTGAGTCGTAT
+
/AAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
@NS500455:80:HG7TNBGXB:1:11101:8821:1057 1:N:0:ATCACG
TATAATAAATATCTAGATCGGAAGAGCACACGTCCGAACTCCA
How to do this. I dont want to use cutadapt.
Kindly help.