Running RNA mats pipeline using fastq files as input ,unable to generate star index folder

Question

[manasa22.reddy]

Hi everyone,

I am trying to understand rmats pipeline for my project.iam trying to run the pipeline with test files provided in the tutorial. I am successful in running the pipeline using bam files .I have problem running pipeline using fastq files, I am confused about star index folder, where do I get star index folder from? The star index folder link mentioned tutorial has many files in it. I am new to NGS tutorial.

python rMATS-turbo-xxx-UCSx/rmats.py --s1 s1.txt --s2 s2.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --bi ~/STARindex/hg19 --od out_test -t paired --nthread 6 --readLength 50 --tophatAnchor 8 --cstat 0.0001 --tstat 6

Any help would be appreciated

Thanks in advance

[WouterDeCoster]

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[vin.darb]

I up this topic because I have a question relative to this

I have done an analysis of alternative splicing using rMATS, with fastq files as input (so the pipeline execute by itself the mapping with STAR)

But recently I have heard about the 2 pass-mode (http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf) that allow to detect novel splicing junctions

MY question is did people compare these two approaches? Is it worth it to restart my analysis with this 2-pass approach, and if so, how to find in the output file predicted splices de novo?

Thank's by advance

Answer 1

[Eric Lim]

As indicated in the documentation under the "Installation" tab at http://rnaseq-mats.sourceforge.net/user_guide.htm#install ,

Obtain STAR genome index for genome by either of the following two ways
- Download pre-built STAR indexes if using Human (hg38, hg19) or Mouse (mm10)
- Build your own STAR index following STAR manual from genome fasta sequence

You can download these indexes from http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/