s_#_sorted.txt files

[caza]

hello,
im a NGS newbie and i have some solexa data from their pipeline v1.3. can the s_#_sorted.txt files be used in MAQ and how?. i believe these files contain reads that map to the genome uniquely.

thank you

[acnoll]

You might be better off using filtered reads from the export file since MAQ gives non unique reads a low mapping quality and thus do not contribute to SNP calling. Also even though the documentation states that sorted.txt contains only uniquely aligning reads I have seen cases where a sorted.txt file contains reads which DO map to more than one location.

[caza]

unique reads

oh ok. so im using the s_#_sequence.txt file in MAQ, i presume this is just as good as the export.txt file? im using the 'match' command with default settings and 'assemble' with -q 10. Is this sufficient to get alignments consisting only of unique reads, i.e reads that map to only one position?.

thanks for your help