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Hi,
We recently ran TRUST4 on some 10x Genomics TCR data using the command
`trust4 -f hg38_bcrtcr.fa --ref human_IMGT+C.fa -1 input/YWI006-VDJ_S1_L001_R1_001.fastq.gz -2 input/VDJ/YWI006-VDJ_S1_L001…
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## Describe your idea for a new feature
Metadata would be automatically populated with the sequencer instrument model. Ideally, the sequencer's serial number (or other identifier) would also be inclu…
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Good afternoon,
In the config file for `MKFQ`, there is a final parameters `Barcode_Length`. In the example files provided by google drive, the barcode length is `54` for the 10x example. I have so…
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```
Python 3.9.12
deeptools 3.5.1
alignmentSieve 3.5.1
```
*******
Dear all,
when I run `alignmentSieve` with `ATACshift` option, but not for all my samples, I get as output a truncated bam f…
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Hi everyone,
I'm planning on using Decontam (prevalence approach) to identify and filter possible contaminants from skin microbiome sequencing data and was wondering if anyone would be able to prov…
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Similar as previous requirement, the results will located in:
/data/COVID_ADHOC/Sequencing/COVID_WGS/Data/USU_First_Batch_low_std_96_361_18/debug
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Hello. Thanks for the helpful repo.
I am trying to understand some of the decisions you all made and wanted to get some clarification. I don't see a step where you pre-filter for ambiguous Ns befo…
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hi,
Can ichorCNA be used to estimate the purity and ploidy of tumor tissue samples? Can it be used to analyze wgs, wes, and panel sequencing data?
If yes, how to adjust the parameters according to t…
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Placeholder ticket with some notes:
```
Seqr-Sample-QC
Sequencing metrics
if it's exome and external
Platform Level Computation
For exome samples
coverage stats, figure out which pl…
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the question may sound stupid but as the title, is it possible to use*** exome sequencing*** result to do ***paternity testing*** using peddy?