tallulandrews / scrnaseqpipeline Goto Github PK

This is a collection of scripts I use (or have used in the past) to process scRNASeq data. They are free to use by anyone else for any purpose, but come with no assurances or guarantees of correctness or functionality. The general workflow is as follows:

0 : Create the appropriate genome for the dataset, and obtain the read files & initial QC
	- Building mapping indexes generally requires ~30Gb of memory for a mouse-sized genome
1 : Split the files by well (cell), Trim reads as appropriate based on QC
2 : Map the reads to the genome
3 : Clean up mapping output & remove duplicates
4 : Mapping QC
5 : Quantify expression
6 : Assemble expression matrix

Finished Pipelines:
00_Kallisto_For_SmartSeq.readme = Smartseq2 + Kallisto (no UMIs) 


Brief Descriptions of Useful files:
0_Extract_barcodes_from_BAM.sh : open the first line of each BAM file and find the barcode (tagged with BC:) - for matching up metadata.

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kiran0991 swatikaushik yanqiangli liusyscholar zhaoning2016 pati-ni dfajar2 hrk2109 haroon123 him72 gyd1990 hqyone aswinssoman flosz latacca ruidong-li daikouxiaojun wangshun1121 boxizhang j9anuary jiuxuan michaelzh24 gnilihzeux bioshare lzlgboy yandgong307 tanminkang zzygyx9119 arsheedganaie gant61 prathyusha-konda summylove strangerzn simingk zqw1103 yuzhenpeng hhaiyu amrr101 poshine dongshengbai rumarova alaminzju thekingofall hengbingao ouqnet xjyx yingstat aalhendi1707 304243504 bobia9991 smiles2011hyc hasihays denvercal1234github whiffen-cann xinghansun qindan2008 huapengqiu jamesben114711 naili-mortadha