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malachig edited this page Nov 16, 2014 · 41 revisions

RNA-seq Flowchart - Module 2

#2-iv. Indexing

###Create a bowtie index

Create a bowtie index for chr22 and the ERCC spike-in sequences and write it to a 'bwt' sub-directory:

cd $RNA_HOME/refs/hg19/
mkdir -p bwt/chr22_ERCC92
bowtie2-build fasta/chr22_ERCC92/chr22_ERCC92.fa bwt/chr22_ERCC92/chr22_ERCC92
cp $RNA_HOME/refs/hg19/fasta/chr22_ERCC92/*.fa $RNA_HOME/refs/hg19/bwt/chr22_ERCC92/
ls bwt/chr22_ERCC92/

To create an index for all chromosomes instead of just chr22 you would do the following:

cd $RNA_HOME/refs/hg19/
mkdir bwt
bowtie2-build fasta/hg19.fa bwt/hg19
mv $RNA_HOME/refs/hg19/fasta/hg19.fa $RNA_HOME/refs/hg19/bwt/

###OPTIONAL ALTERNATIVE Create index files for use with STAR

cd $RNA_HOME/refs/hg19/
mkdir -p star/chr22_ERCC92
STAR --runMode genomeGenerate --genomeDir $RNA_HOME/refs/hg19/star/chr22_ERCC92 --genomeFastaFiles $RNA_HOME/refs/hg19/fasta/chr22_ERCC92/chr22_ERCC92.fa --runThreadN 8 --sjdbGTFfile $RNA_HOME/refs/hg19/genes/genes_chr22_ERCC92.gtf --sjdbOverhang 100

NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.

Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Alignment Free - Kallisto
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 6: Trinity
Module 7: Trinotate
Appendix: Saving Results | Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup

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