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
upload data to dbGap from rc-stor15 with aspera dbGap_aspera_rc-stor15.sh
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
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
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
loop over directories and perform bulk mtDNA calling using mgatk mgatk-bulk-loop.sh