Viewer which shows F & R strand as top & bottom peaks from the sequence line

Question

[heir_of_isildur88]

Hi all,

I found this nice figure which shows the reads of the forward and reverse strand as peaks in the upward and downward direction respectively from the sequence line.

Figure link is https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020079/figure/F1/ and I am referring to the RNA-Seq data in the figure.

Does anyone know which sequence alignment viewer is used to display that kind of figure?

Thank you very much.

[ATpoint]

I think pretty much all of the popular ones can do this. The only thing you have to do is to give the forward strand signals a positive value in the browser track file and the reverse signals a negative one. If you have a bedGraph, it would be column 4 that is of interest. Multiply it by (-1) if the feature is on the reverse strand.

[heir_of_isildur88]

Thank you for your replies.

I will give it a shot by converting it to bedgraph and view it on IGV as I am using a custom virus genome which is not available in UCSC Genome Browser.

Thanks very much again!

Answer 1

[Kevin Blighe]

Hi, it is most likely the UCSC Genome Browser where they have added multiple custom tracks and hidden most of the other default tracks. The easiest way to upload your data to the UCSC is in bedgraph format, with strand-specific read coverage of course.

HOMER has a nice UCSC export function that should work on any aligned BAM file, and it will output strand-specific information if you specify -strand separate.

For forward and reverse read tracks, you should just output forward and reverse reads separately from your aligned BAM into 2 files, and then work these into BED or bedgraph format. To output forward or reverse reads, I believe that you can use SAMtools: Samtools View: Only Forward Or Reverse Strand

Further information about UCSC custom tracks can be found here: http://genome.ucsc.edu/goldenPath/help/customTrack.html

It may take you some reading to see all of the possible ways to display the data, but it is quite a powerful tool. Once you upload your data, you can then even share the URL to collaborators and they can then view the same data until the session expires.

Kevin