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Forum: Bioinformatics 08-02-2018, 02:01 PM
Replies: 313
Views: 101,190
Posted By rmf
Import bedGraph

Is it possible to import bedGraph files? Or more generally speaking can I plot any quantitative data as a track with the following info:

chr start end value

And value being some continuous...
Forum: Bioinformatics 12-20-2017, 09:21 AM
Replies: 3
Views: 2,053
Posted By rmf
Smile BBMap pileup questions

I am interested in metrics that summarise coverage from my BAM file. I came across BBMap pileup which does a decent job. But I have a couple of questions.

1. It seems like if a window is provided...
Forum: Bioinformatics 06-10-2016, 06:29 AM
Replies: 313
Views: 101,190
Posted By rmf
That's a neat little trick. Thanks for that.

That's a neat little trick. Thanks for that.
Forum: Bioinformatics 06-10-2016, 12:39 AM
Replies: 313
Views: 101,190
Posted By rmf
Expand annotations

Its's strange that such a feature is down-weighted. I would think that it is important to see exactly what features your reads are overlapping with. Perhaps not that important when doing a...
Forum: Bioinformatics 06-08-2016, 10:27 AM
Replies: 313
Views: 101,190
Posted By rmf
Expand annotations

Hi Simon,
The annotations overlap a lot and it's hard to read.

http://s33.postimg.org/yt747yxgv/Screenshot_2016_06_08_19_21_05.png

Is there an option to expand annotations like that in IGV?
...
Forum: Bioinformatics 05-17-2016, 01:59 PM
Replies: 313
Views: 101,190
Posted By rmf
Yes! It works now. Thanks a lot.

Yes! It works now. Thanks a lot.
Forum: Bioinformatics 05-16-2016, 10:00 AM
Replies: 313
Views: 101,190
Posted By rmf
Custom Pseudo-chromosomes

I have tried to modify the aliase.txt and chr_list as shown below. I renamed the names in aliases.txt and moved the chr lengths around in chr_list. But when I reopen and create a new project and load...
Forum: Bioinformatics 05-12-2016, 03:05 AM
Replies: 313
Views: 101,190
Posted By rmf
Custom Pseudo-chromosomes

I am creating a new custom genome. I have 25 chr, 1 mt and a whole lot of scaffolds. I can only see automatic pseudo-chromosome creation and it doesn't do exactly what I want. I would like to group...
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