rnaseq
mixcr
| rnaseq | mixcr | |
|---|---|---|
| 1 | 1 | |
| 6 | 311 | |
| - | 2.9% | |
| 3.7 | 9.7 | |
| 20 days ago | 1 day ago | |
| Shell | Kotlin | |
| - | GNU General Public License v3.0 or later |
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rnaseq
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RNA seq bam files help?
A place to start https://github.com/davetang/rnaseq
mixcr
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Is it possible to get tcra data from single cell raw reads? The paper only provides tcrb data.
If you have access to the fqs then there's a chance you can extract some sequences out using Mixcr or similar, but there probably won't be many. You will need the reads because not all of the TCR is germline encoded.
What are some alternatives?
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
hgvs - Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
PyDESeq2 - A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
rnaseqc - Fast, efficient RNA-Seq metrics for quality control and process optimization
galaxy - Data intensive science for everyone.
RNA-seq-analysis - RNAseq analysis notes from Ming Tang
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
alevin-fry - 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.