I have an Ion Torrent Ampliseq Custom panel of 28 Culex genes that I have run on our Ion PGM. It's a small pilot project and I don't need to map against the whole genome (currently in the form of supercontigs), just my fasta file of 28 genes. I'd like to align the reads and get a consensus for each gene.
I have the PGM output as fastq files. Here's what I've done so far: used FastQ Groomer, Filtered those results on their quality scores, converted the FastQ results to FastA, and then mapped those reads using Lastz. I'm mapping the reads to my fasta file that has the sequences of the 28 genes in it.
That all seems to work. If you can see job #52 in my history, you can see the reads and that they are organized by gene (ex. CPIJ005953). I'm having trouble aligning the reads for each gene and then exporting a consensus. It's almost like my output is sort of a SAM file, but not enough of one to convert it to a BAM file. Can anyone advise? The data are for one individual, if that makes any difference.