Illumina reads failing to map to bacterial genome with Tophat

[C9r1y]

Hello,

I am working with fastq files generated from an Illumina HISeq 2000. They are 50bp paired end reads. I am trying to align these files to the Shewanella genome and my results have been discouraging. When I view my accepted_hits.bam files generated from Tophat in the IGV, I see that the coverage is sparse and the reads that are present are not mapping to genes. My tophat command is as follows:

tophat -p 8 -G Shewanella_MR1.gtf -o <outputfile> Shewanella_index Sample1_1.fq Sample1_2.fq

Does anyone know of any parameters that I may be missing that could affect the stringency of the alignment? Thanks for any insight. I have attached a screen shot of the alignment files in the IGV.

[swbarnes2]

Why are you using tophat? Just use Bowtie? Tophat is for aligning transcript reads to a genome. It's purpose is to align reads which are split across exomes. That doesn't happen with bacteria, or with a DNA prep.

[capricy]

well, if tophat doesn't do, do you expect bowtie to be better? tophat is based on bowtie...