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Fatal error: TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed.
chipseq.bds, line 76 : main()
chipseq.bds, line 79 : void main() { // chipseq pipeline starts here
chipseq.bds…
rdali updated
7 years ago
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We'd like to use igv.js for quantitative data in either wig or bedGraph format having both the data and genomes on our own server. This works well as long as no annotation is added (though it would be…
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I'd first like to thank you for your great suite of tools. We are using it very frequently.
I think I have found a bug in bamCoverage when using it in a somehow unusual fashion. I have done the foll…
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Maybe start with bsmap to get through to data/figures, then go back and hit other pipelines.
Timeline wise - looking to have something preliminary next week.
sr320 updated
7 years ago
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When loading flat genome data through “flatfile-to-json.pl”, JBrowse uses some form of heuristic method to generate histograms. Unfortunately, in the absence of sufficient data, the method outputs eit…
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For some reason when I attempt to sort-bed my bedGraph files my chromosome names are converted to a weird annotation of G********\* and the file type changes from text to video.
Using Linux Ubuntu 14…
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Hi,
I've trying to install wiggletools on my desktop. Followed the installation instructions, I installed all pre-requisite package but still can't install wiggletools.
This is the output when I…
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`toil-scripts 2.0.10` on `c3.8xlarge`
It looks like the program sees that it has memory problems and tries to rerun, but deletes some necessary input files, leading to a fatal error:
```
EXI…
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Is it possible to use computeMatrix with scores (--scoreFileName) as BED instead of bigWig file? For example, if I want to see how my ChIP-seq peaks are distributed around TSS. It should make the calc…
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How could you use alignment data (and `samtools`) as well as `bedtools` in your own project?
Provide a least two examples of what said code might look like.
sr320 updated
7 years ago