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README.md
cd.RData
fpm.RData
go.env.RData
knn.RData
pwpca.RData
sg.RData
varinfo.RData

README.md

Author: Jean Fan

DATA

Data downloaded March 16, 2016 Paper GEO SRA (ftp) IDs

Command: export PATH=~/.aspera/connect/bin:$PATH cd sra/ ascp -i asperaweb_id_dsa.openssh -Q -T -k 2 anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByStudy/sra/SRP/SRP066/SRP066834/ .

organize into one folder

mv SRP066834//.sra .

Process just organoid data

see: /groups/pklab/jfan/Projects/Walsh_NPC_AltSplice/R/recreate.R dput(as.character(cell_info[cell_info$tissue_s == "Microdissected cortical-like ventricle from cerebral organoid", "Run_s"])) c("SRR2967437", "SRR2967465", "SRR2967475", "SRR2967495", "SRR2967527", "SRR2967538", "SRR2967549", "SRR2967585", "SRR2967433", "SRR2967434", "SRR2967435", "SRR2967436", "SRR2967438", "SRR2967439", "SRR2967440", "SRR2967441", "SRR2967442", "SRR2967443", "SRR2967444", "SRR2967445", "SRR2967446", "SRR2967447", "SRR2967448", "SRR2967449", "SRR2967450", "SRR2967451", "SRR2967452", "SRR2967453", "SRR2967454", "SRR2967528", "SRR2967529", "SRR2967530", "SRR2967531", "SRR2967532", "SRR2967533", "SRR2967534", "SRR2967535", "SRR2967536", "SRR2967537", "SRR2967539", "SRR2967540", "SRR2967541", "SRR2967542", "SRR2967543", "SRR2967544", "SRR2967545", "SRR2967546", "SRR2967547", "SRR2967548", "SRR2967550", "SRR2967551", "SRR2967552", "SRR2967553", "SRR2967554", "SRR2967555", "SRR2967556", "SRR2967557", "SRR2967558", "SRR2967559", "SRR2967560", "SRR2967561", "SRR2967562", "SRR2967563", "SRR2967564", "SRR2967565", "SRR2967566", "SRR2967567", "SRR2967568", "SRR2967569", "SRR2967570", "SRR2967571", "SRR2967572", "SRR2967573", "SRR2967574", "SRR2967575", "SRR2967576", "SRR2967577", "SRR2967578", "SRR2967579", "SRR2967580", "SRR2967581", "SRR2967582", "SRR2967583", "SRR2967584", "SRR2967586", "SRR2967587", "SRR2967588", "SRR2967589", "SRR2967590", "SRR2967591", "SRR2967592", "SRR2967593", "SRR2967594", "SRR2967595", "SRR2967596", "SRR2967597", "SRR2967598", "SRR2967599", "SRR2967600", "SRR2967601", "SRR2967602", "SRR2967603", "SRR2967604", "SRR2967605", "SRR2967606", "SRR2967607", "SRR2967455", "SRR2967456", "SRR2967457", "SRR2967458", "SRR2967459", "SRR2967460", "SRR2967461", "SRR2967462", "SRR2967463", "SRR2967464", "SRR2967466", "SRR2967467", "SRR2967468", "SRR2967469", "SRR2967470", "SRR2967471", "SRR2967472", "SRR2967473", "SRR2967474", "SRR2967476", "SRR2967477", "SRR2967478", "SRR2967479", "SRR2967480", "SRR2967481", "SRR2967482", "SRR2967483", "SRR2967484", "SRR2967485", "SRR2967486", "SRR2967487", "SRR2967488", "SRR2967489", "SRR2967490", "SRR2967491", "SRR2967492", "SRR2967493", "SRR2967494", "SRR2967496", "SRR2967497", "SRR2967498", "SRR2967499", "SRR2967500", "SRR2967501", "SRR2967502", "SRR2967503", "SRR2967504", "SRR2967505", "SRR2967506", "SRR2967507", "SRR2967508", "SRR2967509", "SRR2967510", "SRR2967511", "SRR2967512", "SRR2967513", "SRR2967514", "SRR2967515", "SRR2967516", "SRR2967517", "SRR2967518", "SRR2967519", "SRR2967520", "SRR2967521", "SRR2967522", "SRR2967523", "SRR2967524", "SRR2967525", "SRR2967526" )

mv -t ../temp/ SRR2967437/ SRR2967465/ SRR2967475/ SRR2967495/ SRR2967527/ SRR2967538/ SRR2967549/ SRR2967585/ SRR2967433/ SRR2967434/ SRR2967435/ SRR2967436/ SRR2967438/ SRR2967439/ SRR2967440/ SRR2967441/ SRR2967442/ SRR2967443/ SRR2967444/ SRR2967445/ SRR2967446/ SRR2967447/ SRR2967448/ SRR2967449/ SRR2967450/ SRR2967451/ SRR2967452/ SRR2967453/ SRR2967454/ SRR2967528/ SRR2967529/ SRR2967530/ SRR2967531/ SRR2967532/ SRR2967533/ SRR2967534/ SRR2967535/ SRR2967536/ SRR2967537/ SRR2967539/ SRR2967540/ SRR2967541/ SRR2967542/ SRR2967543/ SRR2967544/ SRR2967545/ SRR2967546/ SRR2967547/ SRR2967548/ SRR2967550/ SRR2967551/ SRR2967552/ SRR2967553/ SRR2967554/ SRR2967555/ SRR2967556/ SRR2967557/ SRR2967558/ SRR2967559/ SRR2967560/ SRR2967561/ SRR2967562/ SRR2967563/ SRR2967564/ SRR2967565/ SRR2967566/ SRR2967567/ SRR2967568/ SRR2967569/ SRR2967570/ SRR2967571/ SRR2967572/ SRR2967573/ SRR2967574/ SRR2967575/ SRR2967576/ SRR2967577/ SRR2967578/ SRR2967579/ SRR2967580/ SRR2967581/ SRR2967582/ SRR2967583/ SRR2967584/ SRR2967586/ SRR2967587/ SRR2967588/ SRR2967589/ SRR2967590/ SRR2967591/ SRR2967592/ SRR2967593/ SRR2967594/ SRR2967595/ SRR2967596/ SRR2967597/ SRR2967598/ SRR2967599/ SRR2967600/ SRR2967601/ SRR2967602/ SRR2967603/ SRR2967604/ SRR2967605/ SRR2967606/ SRR2967607/ SRR2967455/ SRR2967456/ SRR2967457/ SRR2967458/


Data converted to fastq format March 16, 2016 Using SRA toolkit

Command: module load seq/sratoolkit/2.5.2 snakemake --snakefile /home/jf154/snakepit/sra/sra.snakefile --jobs 999 --cluster 'bsub -q short -W 12:00 -R "rusage[mem=4000]"' mv *.fastq.gz fastq/ mv *.log out/

Alignment with Tophat Quantification with HTSeq

module load seq/htseq/0.6.1 snakemake --snakefile /home/jf154/snakepit/tophat/tophat.snakefile --jobs 999 --cluster 'bsub -q short -W 12:00 -R "rusage[mem=4000]"'