I have been given a FASTQ file of reads, I think from a SOLiD run, with (to me) rather unfamiliar properties (although I am showing my lack of experience with this kind of data here) -- odd quality scores and a lot of "Ns" - here is a sample read....
@hominis_solid:1_6_59/1
NCNTGCNNTNNNNNNTACTTCNNNNAANNANTNNCNACNGNANACGGNC
+
-".-".'<-"-"2-"-"-"-"-"-"3'%)'1-"-"-"-")(-"-")-"'-"-"&-"-%-"%-"(-")%(%-"%
I would like to map these reads to a reference genome and call SNPs. Bowtie 1 and 2 didn't want to do the mapping because they didn't seem to understand the quality scores. I tried mapping using the "raw" option in Bowtie and removing the headers and quality data, but then about 0% of the reads (17 out of 8.3million) would map. Any help greatly appreciated!
