trim leading T or A from fastq file

Question

[meishengxiao86]

Hi, I am working with RNAseq data. I want to trim the leading T or A from my fastq file then perform mapping. Does anyone know how to do that? Thanks a lot!

Meisheng

Answer 1

[Pierre Lindenbaum]

The following awk script should do the job (look at the length of the AT prefix in the 2nd line)

awk '{if(NR%4==2) {L=0;if(match($0,/^[ATat]+/)>0) { L=RLENGTH;} $0=substr($0,L+1);} else if(NR%4==0) {$0=substr($0,L+1);} print;}' in.fastq > out.fastq

[meishengxiao86]

Hi Pierre, Thanks very much for your reply! I have tried the code you supplied, however it seems not workable. The following is the content of the error.

awk: {if(NR%4==2) {L=0;if(match(-bash,/^[Tt]+/)>0) { L=RLENGTH;} -bash=substr(-bash,L+1);} else if(NR%4==0) {-bash=substr(-bash,L+1);} print;}
awk:                                                                  ^ syntax error
awk: {if(NR%4==2) {L=0;if(match(-bash,/^[Tt]+/)>0) { L=RLENGTH;} -bash=substr(-bash,L+1);} else if(NR%4==0) {-bash=substr(-bash,L+1);} print;}
awk:                                                                                                              ^ syntax error

Do you have any idea about this? Thanks!

Meisheng

[Istvan Albert]

make sure to copy/paste the code correctly, it does work