visualizing RNAseq mapping to reference

ssully · 03-04-2019, 03:25 PM

I'm using Geneious (for Windows), which has two RNA Seq mappers (Geneious RNA Mapper, and BBmap). I'm looking for introns in a set of individual gene sequences. Mapping results in Geneious are displayed in several ways, including a coverage track that shows introns plainly. However, there's no way to export this image. I can export output to SAM/BAM files, however. So, what vizualization tool can I use to produce an exportable graph that plots coverage vs nt position?

EDIT: I found that Geneious allows exporting coverage data as .csv or .wig, so I'm good. But I'd still like to know how to generate plots or .csv files automatically for dozens of genes at once.

GenoMax · 03-05-2019, 04:59 AM

You can use Integrated Genome Viewer (Broad Institute) to do batch analyses/exports of images. Details are included here.

IGV-snapshot-automator is another thing you may be interested in.

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03-04-2019, 03:25 PM	#1
ssully Member Location: NYC Join Date: Aug 2010 Posts: 48	visualizing RNAseq mapping to reference I'm using Geneious (for Windows), which has two RNA Seq mappers (Geneious RNA Mapper, and BBmap). I'm looking for introns in a set of individual gene sequences. Mapping results in Geneious are displayed in several ways, including a coverage track that shows introns plainly. However, there's no way to export this image. I can export output to SAM/BAM files, however. So, what vizualization tool can I use to produce an exportable graph that plots coverage vs nt position? EDIT: I found that Geneious allows exporting coverage data as .csv or .wig, so I'm good. But I'd still like to know how to generate plots or .csv files automatically for dozens of genes at once. Last edited by ssully; 03-04-2019 at 03:52 PM.

03-05-2019, 04:59 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	You can use Integrated Genome Viewer (Broad Institute) to do batch analyses/exports of images. Details are included here. IGV-snapshot-automator is another thing you may be interested in.