BICF
Astrocyte

rnaseq

Repository

1) Trim the ends of sequences with remaining adapter or quality scores < 25. Remove any sequence less than 35bp after trimming, then generate a file for capturing information about how many sequences were trimmed.
2) Trimmed Fastq files are aligned to the selected reference genome using HiSAT2 (Kim et al. 2015) or STAR (Dobin et al. 2012)
3) Marks Duplicates using SAMBAMBA
4) Features (genes, transcripts and exons) are counted using featureCounts (Liao et al 2014) and StringTie (Pertea et al. 2015) using the Gencode feature table(Harrow et al. 2012)
5) Basic pairwise differential expression analysis is performed using EdgeR (Robinson et al. 2010) and DESeq
6) Abundances of transcripts are calculated using ballgown (Frazee et al. 2014)
7) Identify gene fusions or fused transcripts using STAR-Fusion.
fastq - Choose one or more RNASeq read files to process.
genome - Choose a genomic reference (genome).
stranded - If a stranded library is created, please select the appropriate protocol to ensure strand specific analysis
markdups - The default is to remove duplicates, you can skip this function.
pairs - Indicate if this is paired-end or single-end sequencing data
dea - Perform Differential Expression analysis, please skip if there are < 2 sample groups
geneset - Select a set of known genesets for pathway analysis
fusion - Perform Gene Fusion Identification
design - This file matches the fastq files to data abot the sample
SampleID
    This ID should match the name in the fastq file ie S0001.R1.fastq.gz the sample ID is S0001
    Note: SampleID shouldn't start with numbers ie 10C should be changed to S10C
SampleName
    This ID can be the identifier of the researcher or clinician
SubjectID
    Used in order to link samples from the same patient
SampleGroup
This is the group that will be used for pairwise differential expression analysis
FqR1
Name of the fastq file R1
FqR2
Name of the fastq file R2