Various and sundry collection of scripts I've used for NGS analysis
Strandededness check for RNA-Seq using ReSQC and Bedops
gene_ID and gene_name extraction from ensembl GTF (Mmus GRCm39 as example) to a tsv conversion table
Extraction of the PWS imprinted domain genes on Mmus Chr7 based on genomic coordinates from ensembl GTF (Mmus GRCm39 as example)
Convert .sam files using samtools sort then index as bin/bash script
short bash scripts to get md5 checksum. used prior to NCBI/Geo upload
script to extract SRXxxxxxxxx IDs from SRA Run Selector Meta data. This was needed for input into nf-core fetchngs rather than synapse IDs.
long one cat/grep/awk/tr/sed one-liner to extract metadata from an .xml file into a simple .tsv