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Old 05-02-2011, 04:08 PM   #1
Kennels
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Default How to separate coverage of forward and reverse reads on same axis?

Hello,

Rather than have to do it in a spreadsheet application, does any know of a visualization software (e.g. IGV, Artemis) or functionality in these software, that is able to plot the coverage of forward and reverse strand reads of .bam files on the same x-axis but have the counts of reverse reads on the negative scale of the y axis?

I have both IGV and Artemis but haven't been able to work out how to do this in them (if even possible).

Any help or advice greatly appreciated.
Thanks,
Kennels
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Old 05-02-2011, 11:30 PM   #2
simonandrews
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SeqMonk can split it's raw data display in the way you describe (as in the screenshot below). You can also quantitate forward/reverse reads separately which would allow you to do a proper quantitation to show this data - although in that case you'd have the forward/reverse split in two adjacent tracks, rather than on a single split track.
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Old 05-03-2011, 12:01 AM   #3
Kennels
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Quote:
Originally Posted by simonandrews View Post
SeqMonk can split it's raw data display in the way you describe (as in the screenshot below). You can also quantitate forward/reverse reads separately which would allow you to do a proper quantitation to show this data - although in that case you'd have the forward/reverse split in two adjacent tracks, rather than on a single split track.
SeqMonk is actually something I've wanted to try for a long time, but from what i've read it can only load supported annotated genomes. I'm actually just working with datasets on very small references (vector constructs, viruses). Is it possible to 'easily' or intuitively import custom genomes locally? I'm not very linux/scripting-savvy as of yet, but can manage simple perl and gff/bed creation etc. Thanks
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Old 05-03-2011, 12:08 AM   #4
simonandrews
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Quote:
Originally Posted by Kennels View Post
SeqMonk is actually something I've wanted to try for a long time, but from what i've read it can only load supported annotated genomes. I'm actually just working with datasets on very small references (vector constructs, viruses). Is it possible to 'easily' or intuitively import custom genomes locally? I'm not very linux/scripting-savvy as of yet, but can manage simple perl and gff/bed creation etc. Thanks
Details of how to create a custom genome in SeqMonk can be found here

It's basically just a head of EMBL format sequence files (with the sequence part being optional), with a somewhat specific format for the accession line. If you're happy doing any kind of scripting it should be pretty simple to create something which works for your dataset. Feel free to contact me directly if you get stuck.
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Old 05-03-2011, 12:44 AM   #5
maubp
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Quote:
Originally Posted by Kennels View Post
Hello,

Rather than have to do it in a spreadsheet application, does any know of a visualization software (e.g. IGV, Artemis) or functionality in these software, that is able to plot the coverage of forward and reverse strand reads of .bam files on the same x-axis but have the counts of reverse reads on the negative scale of the y axis?

I have both IGV and Artemis but haven't been able to work out how to do this in them (if even possible).

Any help or advice greatly appreciated.
Thanks,
Kennels
The Artemis BamView plugin does this. Once you've loaded the data, right click on the read panel, select "Views", "Strand Stack View".
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Old 05-03-2011, 04:40 PM   #6
Kennels
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Maudbp:
Thank you. I am aware of the stacking of reads in this way, but can't seem to find a way to do it for a split coverage plot. Wonder if there's a way to fiddle around this.

Simon:
Thank you, i will try it out! Wonder if there would be functionality in the future to do a split coverage plot.
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Old 05-04-2011, 12:12 AM   #7
maubp
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Quote:
Originally Posted by Kennels View Post
Thank you. I am aware of the stacking of reads in this way, but can't seem to find a way to do it for a split coverage plot. Wonder if there's a way to fiddle around this.
I see the distinction now, I must have read your original post too quickly - sorry.

I'm not aware that the Artemis BamView plugin has that capability. You could get it indirectly by using the SAM/BAM file to make two coverage plots for the two strand (e.g. wiggle files or one of the other formats Artemis supports), but that is cumbersome.
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