{"repo":"sanjaynagi/rna-seq-pop","free":true,"listed":false,"github":"https://github.com/sanjaynagi/rna-seq-pop","clone":"git clone https://github.com/sanjaynagi/rna-seq-pop.git","description":"Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data","language":"Jupyter Notebook","stars":18,"topics":["snakemake-workflow","rna-seq","variant-calling","differential-expression","population-genomics","snakemake","transcriptomics","workflow","population-genetics","selection"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Documentation : https://sanjaynagi.github.io/rna-seq-pop/ Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4M RNA-Seq-Pop is a computational pipeline to analyse Illumina RNA-Sequencing data of any organism. As well as performing standard transcriptomic analyses, such as differential expression, RNA-Seq-Pop also calls and analyses genetic polymorphisms, extracting population genomic signals. The workflow can perform the following analyses of illumina paired-end RNA-Sequencing data: Quality control of fastq reads with fastqc, QC metrics integrated into a final report with multiQC Differential expression analysis with Kallisto at the gene level (DESeq2) and transcript level (Sleuth), and gene set enrichment analyses. Variant calling with freebayes Fst and Population branch statistic (PBS), both in windows across contigs and at the gene-level (Scikit-allel). Allele frequencies at variants of interest (pre-specified loci of choice). Various summary statistics (Wattersons Theta, Sequence Diversity, Dxy etc) Analysis of Ancestry Informative Markers (AIMs) to determine relative ancestry of An.gambiae/coluzzii/arabiensis ( Anopheles gambiae s.l ) Determines Karyotype of chromosomal inversions using compkaryo ( Anopheles gambiae s.l ) The workflow is generalised, and will function with any Illumina single or paired-end RNA-sequencing. However, certain modules, such as the ancestry and karyotyping, are only appropriate for An. gambiae s.l . These can be activated in the configurat","default_branch":null,"files":null,"tree":[],"storefront":"/r/sanjaynagi","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/sanjaynagi/rna-seq-pop/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}