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Hi MIXCR team,
We have a series of fastqs containing Unique Molecular Identifiers (UMIs). These fastqs are from hybrid-capturing of CDR3 regions of TCR (genomic DNA).
Since troubleshooting of the pi…
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In CCDH, we're trying to create a mapping from the NCI nodes' data dictionaries to NCIt codes that will be used in the common model. For example, in NCI GDC (genomic data commons) data model Aliquot, …
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Hi,
This pipeline is helping me so much.
I am using this pipeline to analyze Fragmentation Profile Analysis.
CODE
```from cfDNApipe import *
import glob
pipeConfigure2(
threads=60,
…
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Hello everyone,
I am quite new to the ONT basecallers and i am trying to use megalodon on our HPC to analyze some cfDNA samples.
I installes megalodon on the HPC via pip an the OS is Linux. I …
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# 生信爱好者周刊（第 38 期）：
这里记录每周值得分享的生信相关内容，周日发布。
本杂志开源（GitHub: [ShixiangWang/weekly](https://github.com/ShixiangWang/weekly)），欢迎提交 issue，投稿或推荐生信相关内容。
[「生信周刊讨论区（语雀）」](https://www.yuque.com/shixiangw…
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Megaldon/2.4.2
modbam2bed/0.4.0 (https://github.com/epi2me-labs/modbam2bed)
samtools/1.14
I am running Megalodon in CG remora mode ("--remora-modified-bases dna_r9.4.1_e8 hac 0.0.0 5mc CG 0 --gu…
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testbam=/bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/0_Illumina_UMI_Error_Corrected_bam/Sample1.collapsed.bam
hg19_fasta=/bgfs/soesterreich/pan_…
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If cfDNA pipeline is started with steps mapping and db only the step db will crash. The pipeline does not find the files *FO13585x01_01_stats_cfDNA. This file is created by the "vc" step.
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I use the same bashrc setting in three servers, the code can be run successfully, but showed a broken pipeline in one server. The samtools(samtools-1.14), python(python3.9) and bwameth all the same. …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/CTrierMaansson/DNAfusion
Confirm the following by…