Visualize raw rna fastq file and aligned bam file

Question

[shinyjj]

Hi, I am trying to see how raw rna fasq and aligned bam file look like by any visualization tools. Are there any tools to visualize fastq files? Furthermore, are there any tools to see what the mapped bam file looks like (e.g. which transcript or gene it's mapped to) after aligning fastq file using tools like STAR or minimap2? I am not sure if genome browser is related to this. I am quite new to this area, so any suggestions are welcome!

Answer 1

[GenoMax]

There are multiple genome browsers available (standalone or online). IGV - Integrative genomics viewer is one of the more commonly used tools that you can install on PC/Mac/Unix. https://igv.org/doc/desktop/ Excellent user guide is available at this site to get you started.

Other examples are IGB, tablet etc.

Are there any tools to visualize fastq files?

There is nothing to visualize in raw sequence files. You will simply have millions of sequence records in fastq format.

Answer 2

[Alex Reynolds]

The main HiGlass client-side piece can be integrated with a track plugin called higlass-pileup, which renders reads in a BAM file aligned to a specified assembly. You can pan and zoom to view reads as well as a coverage track.

Indexed BAM files can be hosted on any web server, e.g. a common local nginx host all the way to S3/Cloudwatch, etc.

Other track plugins that could be useful to add to the HiGlass container are higlass-transcripts and higlass-sequence.

The transcripts plugin in its current form requires a higlass-server instance to serve processed gene annotation data. A server can be instantiated via higlass-manage.