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Hi,
**Use case**
I am using ATAC-seq data from plants materiels with 3 replicates. The data set was build on more or less 60K of cell in differents tissues.
**Describe the problem**
First I la…
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Greetings,
I am interested in using this pipeline to remove haplotigs from a PacBio assembly. I am following the Pipeline Guide (Steps 1-3). I have a few questions regarding my output.
I assume…
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Hi!
I am trying to incorporate bcbio-vc docker image onto my pipeline manager and for that I am trying to run and test variant calling on `bcbio-vc` docker image but I see that `bcbio_nextgen.py` i…
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Hello,
Thank you for developing this tool. I am trying to quantify transcript abundance using direct RNA seq reads after mapping with minimap2 to a transcriptome that I got using FLAIR and SQANTI too…
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Hi Chris,
I am attempting to implement iRep for a single metagenomic reconstruction and a very large sam file (36 G). The default thread behaviour is listed a 6 threads, but top reveals I am only usi…
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**Describe the bug**
It seems like neat processes regions in the reference that I did not explicitly include in the target bed file. I want to simulate reads for some cancer related genes using the…
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### Problem Description
Currently, rotary gives every multithreaded rule the complete set of CPU threads. However, these jobs often only sometimes use all these available threads all the time. For …
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Hi.
In the Michigan Imputation Server pipeline page (http://imputationserver.readthedocs.io/en/latest/pipeline/), the Minimac4 command is using --meta and --minRatio in Minimac4?
However, I ca…
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Hi,
In the paper “Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis” , we failed to find the polish step of the haplotype-resolved …
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collecting references and annotations --
1. [VarCover: Allele Min-Set Cover Software](https://www.sciencedirect.com/science/article/abs/pii/S1525157819304143)
>To facilitate reference-material s…