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Old 03-08-2013, 04:18 PM   #1
C9r1y
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Default Illumina reads failing to map to bacterial genome with Tophat

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.
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File Type: pdf Shewanella_alignment_IGV.pdf (67.0 KB, 14 views)
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Old 03-08-2013, 07:25 PM   #2
swbarnes2
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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.
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Old 12-07-2015, 07:51 AM   #3
capricy
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well, if tophat doesn't do, do you expect bowtie to be better? tophat is based on bowtie...
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