Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Genome Res De novo bacterial genome sequencing: millions of very short reads assembly b_seite Literature Watch 1 10-04-2017 11:26 PM
using bwa to map illumina paired end reads mikeworth Bioinformatics 6 08-13-2013 06:02 PM
Tophat problem: failing reads alignment Annibal RNA Sequencing 6 05-18-2012 12:34 PM
TopHat 1.1 failing on colorspace SE reads krobison Bioinformatics 22 09-22-2011 11:25 AM
How to map short reads to a distant genome? ynwh Illumina/Solexa 5 08-03-2011 05:56 AM

Thread Tools
Old 03-08-2013, 03:18 PM   #1
Junior Member
Location: San Francisco, USA

Join Date: Jan 2013
Posts: 8
Default Illumina reads failing to map to bacterial genome with Tophat


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.
Attached Files
File Type: pdf Shewanella_alignment_IGV.pdf (67.0 KB, 14 views)
C9r1y is offline   Reply With Quote
Old 03-08-2013, 06:25 PM   #2
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

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.
swbarnes2 is offline   Reply With Quote
Old 12-07-2015, 06:51 AM   #3
Senior Member
Location: 63130

Join Date: Apr 2012
Posts: 125

well, if tophat doesn't do, do you expect bowtie to be better? tophat is based on bowtie...
capricy is offline   Reply With Quote

alignment, illumina, paired end mapping, tophat

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 01:36 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO