useful scripts

sratoolkit

download data from NCBI GEO on O2 prefetch-O2.sh

download data from NCBI GEO using list of libraries on O2 prefetch-list-O2.sh

dbGap

upload data to dbGap from rc-stor15 with aspera dbGap_aspera_rc-stor15.sh

salmon

gene quantification with salmon tools on paired-end data on O2 salmon-paired-end-O2.sh

gene quantification with salmon tools on single-end data on O2 salmon-single-end-O2.sh

create TPM matrix from salmon tools output generate-TPM.R

TRUST4

run TRUST4 and extract TCR from single-end data on O2 with alignment TRUST4-O2-single-end.sh

run TRUST4 and extract TCR from paired-end data on O2 without alignment TRUST4-O2-paired-end.sh

alignment

realign hg19 to hg38 on O2 realign_hg38.sh

quick hack to quantify single nucleotide polymorphisms or indels primitive-pileup.py

loop over NCBI GEO data and align align-hg38-single-end.sh align-hg38-paired-end.sh

mtDNA

loop over directories and perform bulk mtDNA calling using mgatk mgatk-bulk-loop.sh