qcAndSalmon: Runs the qc and salmon pipeline used by processSRA

In pcahan1/CellNet: Assess and improve cell fate engineering with network biology

Runs the qc and salmon pipeline used by processSRA

Description

Fetch raw sra files named in sampTab and convert to fastq (using SRA toolkit), trim reads to standard length, run QC by aligning sub-sampled fastq files aginst several genomes (human, mouse, zebrafish, fly, ecoli, yeast), and counting hits to genomic features of the target genome. Finish by estimating gene expression levels with Salmon.

Usage

qcAndSalmon(sampTab, studyID, bucket = "cellnet-rnaseq",
  finalLength = 40, subProp = 0.001, target = "mouse",
  gtfFile = "/media/ephemeral1/dat/ref/Mus_musculus.GRCm38.83.gtf",
  salmonIndex = "/media/ephemeral1/dat/ref/MM_GRCh38.SalmonIndex.030816")

Arguments

sampTab	sample table
studyID	study id
bucket	S3 bucket where to put the results
finalLength	final length of reads
subProp	proportion of reads to sample from for QC
target	species/genome for expression estimates
gtfFile	genomic feature of target genome for QC
salmonIndex	path to salmon index for expression estimation

Value

sample table with QC measures appened

pcahan1/CellNet documentation built on May 18, 2023, 4:58 p.m.