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I propose migrating the duplicate marker, BQSR engine, and indel realigner out of ADAM. I would suggest migrating them into [avocado](https://www.github.com/bigdatagenomics/avocado); @massie had also …
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(cc @lbeltrame )
I need to re-run the pipeline without file realignment, since they were previously generated. Setting the parameter aligner to false does not allow to bypass realignment and raises…
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Hi Paul,
We have decided to have a local version of the genome browser, because we have been getting a lot of data (RNA-seq, ChIP-seq and ATAC-seq) which we want to be able to easily visualize. We wou…
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Hi, all
I wondering about the bcbio-nextgen's next plan.
I really hope to contribute the another workflow (like metagenome, de novo assembly, epigenome) in bcbio.
💃
hmkim updated
8 years ago
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```
The guidelines for this have been recently revised several times, so we need to
reformulate levels. Steps:
1) Define levels and file formats (ben)
2) Create sample MAGE-tab (ben)
3) Submit to A…
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Hello
I am using the latest version of deepTools and I am running through this error while running the {compute, correct}GCBias pair :
```
Traceback (most recent call last):
File "/genesis/extsc…
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In chip-seq pipelines the bottleneck is often read deduplication.
The current fastest way, AFAICS, is just using `sort -u k....`.
Do you think this is something that can be done much more quickly in…
ghost updated
9 years ago
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I can see more and more people getting quite involved with helping @pcingola debug BDS and provide suggestions. I am wondering if it would be an appropriate time for someone to create some kind of co…
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Hi,
I use a nitrogen_max board with yocto build image (fsl-community-bsp, current master, 3.10.31 kernel) with an 8-channel PCIe frame grabber (v4l2src using videobuf2) and tried to record 8 streams:…
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Reference alignment builds for TST1 currently can not get past the ref-cov step because an input software result is missing. Specifically, the ref-cov step needs a feature-list result to run properly…