Dropseq_pipeline_setup.Rmd

---
title: "Drop_seq_pipeline_setup"
author: "Sebastian Pott"
date: "8/26/2017"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

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```{bash obtain_ref_genomes}


#hg38
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz .
#combine into one single drop alternative haplotypes (_alt)
tar xvzf hg38.chromFa.tar.gz
cd chroms
rm *_alt.fa
cat *.fa > ../hg38_UCSC/hg38_ucsc.fa
rm -r chroms

#mm10
#chromFa.tar.gz - The assembly sequence in one file per chromosome.
#    Repeats from RepeatMasker and Tandem Repeats Finder (with period
#    of 12 or less) are shown in lower case; non-repeating sequence is
#    shown in upper case.

rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz . 
#combine into one single drop alternative haplotypes (_alt)
tar xvzf chromFa.tar.gz
cat *.fa > mm10_UCSC/mm10_ucsc.fa
rm *.fa

Release 27 (GRCh38.p10)
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.annotation.gtf.gz


Release M15 (GRCm38.p5)
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M15/gencode.vM15.annotation.gtf.gz


#Danio ri.. zebrafish

rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.fa.gz .

gunzip danRer10.fa.gz
# downloaded danRer10 from UCSC
RefGene_danRer10-2017-08-28.gtf 



```



```{bash prep_STAR_indeces}
#dropseq reads are ~50bps lonng hence sjdbOverhang = 49

STAR --runThreadN 2 --runMode genomeGenerate --genomeDir hg38_noalt_juncGencodeV27_49 --genomeFastaFiles hg38_UCSC/hg38_ucsc.fa --sjdbGTFfile hg38_UCSC/gencode.v27.annotation.gtf --sjdbOverhang 49

hg38_noalt_juncGencodeV27_49 


#dropseq reads are ~50bps lonng hence sjdbOverhang = 49
STAR --runThreadN 2 --runMode genomeGenerate --genomeDir dr10_noalt_juncRefGene_49 --genomeFastaFiles danRer10_UCSC/danRer10.fa --sjdbGTFfile danRer10_UCSC/RefGene_danRer10-2017-08-28.gtf --sjdbOverhang 49

#and index includeing fluorochromes
Sebastians-Mac-Pro:STAR_indeces Sebastian$ STAR --runThreadN 2 --runMode genomeGenerate --genomeDir dr10_noalt_juncRefGene_RG_49 --genomeFastaFiles danRer10_UCSC_RG/danRer10_RG.fa --sjdbGTFfile danRer10_UCSC_RG/RefGene_danRer10-2017-08-28_RG.gtf --sjdbOverhang 49



```


```{bash drop_seq_test_run}

#get some of the macosko data:
/sra/sra-instant/reads/ByExp/sra/SRX/SRX907/SRX907219/SRR1853178/

```

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