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I downloaded a patient's scrna count raw data as well as the scVDJ, scRNA sequence data from GEO, and ran './run-trust4 -f human_IMGT+C.fa --ref human_IMGT+C.fa -u xxx_r2.fastq.gz --barcode xxx_r1.fa…
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Webservice that chooses a reference sequence based on
Input:
1) HLA (or other) consensus sequences. full length or features.
2) IMGT version.
Output:
1) Best matching reference sequence
2) …
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I registered a glstring "HLA-A*02:01:01:01+HLA-A*24:02:01:05" in 3.24.0 gl service and used the liftover service to make it 3.25.0, but glstring became an HLA-DPA allele + an HLA-A allele.
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I noticed that the py-ard implementation for converting v2 to v3 typings is not yet complete:
https://github.com/nmdp-bioinformatics/py-ard/blob/d43a035361cc90cef9bf0c98475ec90396b06a4f/pyard/db.py…
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Hello,
I have 2 10X Genomics datasets (BCR and GEX). What are the appropriate parameters setting for TRUST4?
I'm using
f"run-trust4 -1 {f1} -2 {f2} --barcode {f1} --UMI {f1} --readFormat bc:0:15,…
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When initializing py-ARD, HLAGenie currently downloads the NMDP multiple allele code file, which can be problematic when running jobs in parallel on separate nodes of a supercomputer. The downloads of…
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How can I update PRG_MHC_GRCh38_withIMGT data package? I want to change graph to new version of IPD-IMGT/HLA database and leave in graph only alleles with complete CDS.
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Sorry, but I can't seem to understand the instructions from the README file.
It would be great if you could explain it once more. I'd like to use the latest databases from IMGT, but it seems that IMo…
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Hello team,
We recently processed some T-cells samples with the Takara SMART-Seq Human TCR (with UMIs).
We used the command "run-trust4 --barcodeLevel molecule -f $Genome/hg38_bcrtcr.fa --ref $…
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I am running complete analysis using hg38, but get the following error. Your suggestion will be very useful
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[9] Making reference panel for HLA-AA, SNPS,HLA, and Normal variants (SNPs) is…