[cliff]

Hi, golharam and simonandrews

Thanks! I am using WinXP. I will try to run SeqMonk on my desktop first to see if it works.

-c

[natstreet]

This week I discovered that using BigWig files for coverage data works really nicely in GBrowse.

I would really love to have a simple plotting tool to take per chromosome coverage data from something like a BigWig file and plot a nice looking coverage figure. I'm thinking of coding it myself in (probably) python or (maybe) R but if anyone can point me to examples to get started that would be great. Although some genome browsers make coverage plots, they just don't look nice for publication use IMHO.

[drio]

I'd use circos and it's 2d tracks.

[cliff]

Hi, simonandrews

I just noticed that the SeqMonk Release Notes talks about SeqMonk v0.12.0 but it seems I can only find SeqMonk v0.11.0 online. Do you know where to find v0.12.0?

Thanks

[natstreet]

I can see v0.11.0 listed at their website and if you swap 11 to 12 in the download URL there is something there to be downloaded

http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/seqmonk_v0.12.0.zip

[simonandrews]

Hi, simonandrews

I just noticed that the SeqMonk Release Notes talks about SeqMonk v0.12.0 but it seems I can only find SeqMonk v0.11.0 online. Do you know where to find v0.12.0?

Sorry, I'd failed to copy over the new version of the download page from our staging server. If you try again now the links should be in place (if you don't see them press shift+refresh in your browser to force a cache update).

Simon.

[arnoldliao]

IGV scripting function

Use IGV to output plots of a region of a bam file with the following sample script

http://www.broadinstitute.org/igv/batch

attached is an example (note path to bam and snapshotDirectory need to be absolute not relative)

new
load myfile.bam
snapshotDirectory mySnapshotDirectory
genome hg18
goto chr1:65,289,335-65,309,335
sort position
collapse
snapshot

[quinlana]

Use IGV to output plots of a region of a bam file with the following sample script

http://www.broadinstitute.org/igv/batch

attached is an example (note path to bam and snapshotDirectory need to be absolute not relative)

new
load myfile.bam
snapshotDirectory mySnapshotDirectory
genome hg18
goto chr1:65,289,335-65,309,335
sort position
collapse
snapshot

<shameless plug>
Note that BEDTools has a tool called bedToIGV that will automatically create an IGV batch script from a BED, GFF, or VCF file.
</shameless plug>

[bioinfosm]

good one Aaron! I keep using BEDTools more