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Python 2.7 [will not be maintained past 2020](http://pythonclock.org/).
Add support for Python >= 3.3 while maintaining support for Python 2.6 and 2.7.
xref.: https://trello.com/c/dZcCVf9I/2702-migr…
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The program core dumps when I run it on a training set. If you need, I can provide the input files.
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Though I can successfully execute Q on the BAM file suggested in the Tutorial (http://charite.github.io/Q/tutorial.html), the program crashes on my own BAM file. I'm on CentOS.
```
(DK)[dkelley@dkell…
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This is a feature request to lower the disk footprint of a bismark_methylation_extractor run.
I ran master branch including the options `--cytosine_report --gzip --bedGraph` and I was glad to see tha…
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Read bedGraph file, ignore _track definition lines_
http://genome.ucsc.edu/goldenpath/help/bedgraph.html
https://github.com/oncogenetics/LocusExplorer/blob/master/server.R#L98
Related issue: https:…
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I have written a new fast medium/diffuse area chip-seq caller in Python. It uses a binning strategy and one of the files it produces contains the island counts:
```
Chromosome Bin Chip1 Chip2 Input1 …
ghost updated
8 years ago
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I've noticed coverage is wrongly displayed from BAM files for spliced alignments. You expect no or lower coverage for introns than for exons.
http://zdglab.iimcb.gov.pl/jbrowse/?data=data%2FGRCz10&t…
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Short check list for all things we need to do before and after we release.
- [x] tag a github release [Fidel]
- [x] upload to pypi [Fidel]
- [x] conda build [Bjoern or Devon]
- [x] Galaxy TTS and MTS …
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```
What steps will reproduce the problem?
1. Load a sample bam and chr-sizes files from our ftp server
ftp://ftp2.cshl.edu/gingeraslab/tracks/BEDtools/ex1.bam
ftp://ftp2.cshl.edu/gingeraslab/tracks/…
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Dear Author,
What is the best way? I dont want to create a binned file (I want the maximum resolution). Which tool do you usually use for converting bam files to one of the required in seqplots?
Thank…