Maq sol2sanger and solexa paired end reads

[Rick]

Hi ,

am trying to format the solxa seqs from pipleine1.3 with sol2sanger...but i get a "segmentation fault" error whren i try to do it

$ maq sol2sanger s_4_2_sequence.txt s_4_2_sequence.fastq
Segmentation fault

it works fine with single reads seqs

have tried with maq v 0.7.1 and 0.7

any ideas why this is

thanks folks

Rick

[Torst]

This other thread claims that Illumina has changed the quality value mapping in Pipeline 1.3:

http://seqanswers.com/forums/showthread.php?t=1110

Could that be causing the problem?

We are just starting our first 1.3 run, so I'll check out the output files in a week or so.

[fadista]

sol2sanger

Hi,

Just want to be sure here:

1 - Is the sol2sanger function of maq 0.7.1 not working for solexa pipeline 1.3?

2 - If not, how can I convert the scores that I already computed (sol2sanger of maq 0.7.1 with solexa pipeline 1.3) to the sanger phred score system?


Best regards,
João

[rallapag]

Hello,
follow the link to get your pipeline 1.3 fastq to sanger fastq coversion

http://seqanswers.com/forums/showpost.php?p=4426&postcount=2

Thanks
S