GitHub - brianpenghe/linuxshell-genomics: A set of basic scripts to handle genomics tasks using linux shell

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A set of basic scripts to handle genomics tasks using linux shell

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Name		Name	Last commit message	Last commit date
Latest commit History 59 Commits
10X2snap.sh		10X2snap.sh
BaseMountLira.sh		BaseMountLira.sh
CellRangerATAC.sh		CellRangerATAC.sh
CellRangerRun.sh		CellRangerRun.sh
CellRangerVDJ.sh		CellRangerVDJ.sh
CellrangerATAC_at_farm.sh		CellrangerATAC_at_farm.sh
CellrangerSummary.sh		CellrangerSummary.sh
CellrangerVDJSummary.sh		CellrangerVDJSummary.sh
CheckFastqgzs.sh		CheckFastqgzs.sh
CheckFastqs.sh		CheckFastqs.sh
CompressVCF.sh		CompressVCF.sh
Extract3primeFromFastq.sh		Extract3primeFromFastq.sh
FlagBAM.py		FlagBAM.py
GetSeqAFromB.sh		GetSeqAFromB.sh
HCAupload-ATAC.sh		HCAupload-ATAC.sh
HCAupload.sh		HCAupload.sh
InstallBaseMount.sh		InstallBaseMount.sh
KrisStarsoloSummary.sh		KrisStarsoloSummary.sh
PlateTo10XFastq.sh		PlateTo10XFastq.sh
SubsetCellrangerBam.sh		SubsetCellrangerBam.sh
cramfastq.sh		cramfastq.sh
cramfastq10XATAC.sh		cramfastq10XATAC.sh
fix-souporcell-vcf-for-cellranger2020A.sh		fix-souporcell-vcf-for-cellranger2020A.sh
iRODS_download_path.sh		iRODS_download_path.sh
iRODSdownloader.sh		iRODSdownloader.sh
iRODSdownloaderBCR.sh		iRODSdownloaderBCR.sh
iRODSdownloaderTCR.sh		iRODSdownloaderTCR.sh
iRODSdownloader_10XATAC.sh		iRODSdownloader_10XATAC.sh
iRODSdownloader_10XATAC_CellRangerATAC.sh		iRODSdownloader_10XATAC_CellRangerATAC.sh
iRODSdownloader_10XATAC_CellRangerATAC_big2farm.sh		iRODSdownloader_10XATAC_CellRangerATAC_big2farm.sh
iRODSdownloader_CellRangerRunGEX.sh		iRODSdownloader_CellRangerRunGEX.sh
iRODSdownloader_CellRangerRunGEX5prime.sh		iRODSdownloader_CellRangerRunGEX5prime.sh
iRODSdownloader_CheckMeta.sh		iRODSdownloader_CheckMeta.sh
iRODSshowLane.sh		iRODSshowLane.sh
souporcell_all.sh		souporcell_all.sh