[maq-help] maq map command - getting no alignments

[Amit I. <in...@gm...>]

Hello,

I am a maq newbie. I have 4 lanes of Solexa data on yeast (each lane
anywhere from 3.9M to 4.7M reads) My original sequence files were
generated from the solexa pipeline and in s_*_sequence.txt files. I
converted them with the maq sol2sanger command successfully.
I also prepared my reference genome  successfully with the command

>maq fasta2bfa sacCerv1.fa  sacCerv1.bfa

However, when I run the match command maq doesn't align *any* of my
reads to the reference:

>maq map out.map /Genomes/sacCerv1/sacCerv1.bfa s_1.bfq

output:
[ma_load_reads] 4174651*2 reads loaded.
[mapping_count_single] 0, 0, 0, 0
[maq_indel_pe] the indel detector only works with mate-pair reads.
[match_data2mapping] 0 out of 8349302 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (4174651, 0, 0, 0)

So it isnt' mapping any of the reads. Am I missing an option? I don't
have any mate-pairs in my data. If you can point me in the right
direction, that would really helpful.

Thanks,

Amit


-- 
Amit Indap
Biological Statistics & Computational Biology
Cornell University