rnaseq
rnaseqc
| rnaseq | rnaseqc | |
|---|---|---|
| 1 | 1 | |
| 6 | 140 | |
| - | 1.4% | |
| 3.7 | 4.5 | |
| 20 days ago | 24 days ago | |
| Shell | C++ | |
| - | 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
rnaseqc
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Tools for strand direction detection RNA-Seq
I like to use RNA-SeQC (https://github.com/getzlab/rnaseqc). It shows the percentage of forward/reverse reads that alingned to either the sense or antisense strands. It is also compatible with multiQC which is a big plus.
What are some alternatives?
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
PyDESeq2 - A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
TPMCalculator - TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
RNA-seq-analysis - RNAseq analysis notes from Ming Tang
how_are_we_stranded_here - Check strandedness of RNA-Seq fastq files
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
popscle - A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
mixcr - MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.