Conversion of qseq.txt format to fastq

[rakeshponnala]

Hello Folks,

Could any one please let me know,if their is a way to convert the qseq.txt format files of illumina to fastq format. I finished my run and I would like to align my reads to ref seq using MAQ. MAQ requires the read data to be in fastq. Currently I've my data in qseq.txt format.

Any suggestions would be greatly appreciated.

Thank you

Rakesh

[kmcarr]

Using the forums search tool would have found these threads:

http://seqanswers.com/forums/showthread.php?t=1801

http://seqanswers.com/forums/showthread.php?t=1655

[dukevn]

You can try the following one liner in Bash: go to where those _qseq.txt files locate, and if those qseq.txt are in form of s_N_1_M_qseq.txt where N is lane number (1-8), M is tile number (1-120), then

$ for ((x=1;x<=8;x+=1)); do cat s_"$x"_1_*_qseq.txt | awk -F '\t' '{gsub(/\./,"N", $9); if ($11 > 0) printf("@%s_%04d:%s:%s:%s:%s#%s/%s\n%s\n+%s_%04d:%s:%s:%s:%s#%s/%s\n%s\n",$1,$2,$3,$4,$5,$6,$7,$8,$9,$1,$2,$3,$4,$5,$6,$7,$8,$10)}' > s_"$x"_sequence.fastq; done

The resulting s_N_sequence.fastq (N is 1->8) are the 8 fastq files you will need.

[rakeshponnala]

Hi Dukeven,

On the Unix machine, I went to the directory where my qse.txt file were and typed in the command Bash and pasted your code

$ for ((x=1;x<=8;x+=1)); do cat s_"$x"_1_*_qseq.txt | awk -F '\t' '{gsub(/\./,"N", $9); if ($11 > 0) printf("@%s_%04d:%s:%s:%s:%s#%s/%s\n%s\n+%s_%04d:%s:%s:%s:%s#%s/%s\n%s\n",$1,$2,$3,$4,$5,$6,$7,$8,$9,$1,$2,$3,$4,$5,$6,$7,$8,$10)}' > s_"$x"_sequence.fastq; done

It shows:

syntax error near unexpected token `('


I'm new so....... not sure why it doesn't work

Thanks

[dukevn]

It works just fine here. Dont know why you got that error. Just to be sure that the command should be in one line only in your terminal.

[GRT]

rakeshponnala you had this $ 5 instead of $5

[bbm]

I ran the script, and msg is "syntax error near unexpected token `('"

[barkasn]

Maybe I am missing something, but why don't you use the normal Illumina pipeline with Casava?