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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.
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.
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