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Consider:
- extracting all reads aligning to chrM
- filtering reads with primary/supp alignments elsewhere (NUMTs)
- realign with an aligner aware of circular references ([graphmap](https://github.…
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Hi @genegodbold
We have terms for these for viruses:
- PATHGO:0000302 | disrupts JAK-STAT signaling in another organism [Gene--I provide eukaryotic and bacterial examples below]
- PATHGO:0000…
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### Description of the bug
My RNA-seq datasets were captured by TrueSeq ranther than by PolyA, so I set parameter --gene_bed manually. The TrueSeq bed only has 4 columns:
```
browser position chr1:…
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### Description of the bug
Could you please see below error that happened every time I re-run the pipeline. I was about to send the log file, but there are too many as I have repeated this run many t…
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### **Description**
I wish to use the latest NanoSim v3.0.1 (supports reading .gz sequence files, and bam files), but `read_analysis.py` does not complete. The `primary.bam` file is not indexed, an t…
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Hi team,
I found the `-z` length filtering is not working as expected.
I have run some data using command
```
pychopper -t $num_cores -Q 7 -z 50 \
-r ${base}_report.pdf -S ${base}_statisti…
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https://mp.weixin.qq.com/s/F81LzNgrk4hFpEXDm_1E-A
ixxmu updated
1 month ago
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### Installation Type
Standalone
### pVACtools Version / Docker Image
4.0.1
### Python Version
3.8.3
### Operating System
Centos7
### Describe the bug
Hi Susanna,
I got an …
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Dear Nanopore Developers,
Please restore the Nvidia Pascal GPU achitecture support (sm_61) for Koi Library v 3.1.0 used by the dorado 0.3.0 basecaller
GPU's with this architecture is still widely …
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### Goal
[remaining volume](https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecpart_attribute_type#remaining_volume) - Amount of tissue or extract remaining in a vial. Used to he…