RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
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Updated
Jun 14, 2024 - Python
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto
Map and post-process your bams for SNP calling
Count your fastq-formatted rna-seq reads with Salmon
Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, …
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Tools to analyze fasta or fastaq files with python.
A Snakemake workflow for quality control assessment of Illumina NGS data using FastQC and MultiQC
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A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards
A Snakemake Workflow for using PolyA_DB and UCSC LiftOver with CellRanger
A python package for working with inputs to and outputs from the toil-rnaseq pipeline
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