How to map NCBI SOLiD reads with BWA

[Chandana]

Hi,
I have downloaded some SOLiD reads from NCBI and needs to map them using BWA. Should I simply convert 0->A, 1->C etc. or do I need to chop the first two bases in addition?

[Chipper]

If you really need to use BWA you have to use the solid2fastq.pl script that comes with it. You also need to change the parameters to increase the number of mismatches allowed.

[Chandana]

Thanks Chipper for the quick reply, but the script does not seem to work on my case. the reads are like


@ERR012630.16 VAB_solid0029_20100115_QR1000044_50X2_QR10000441_14_61/1
T0010..330..00013.00.0.20...00.0..02..0000..00.....
+
!/95%!!<).!!:%,/)!17!9!54!!!45!-!!!!68!!9;!!!!!

but the scripts expects the quality values and the reads separated. Can you help me in this case?

[Chipper]

Ok, since it is FastQ already you could just change 0123 to ACGT and remove the first two bases as you suggested. You could also try bowtie, it's faster and I think it will accept the file as is.