Question: Running RNA mats pipeline using fastq files as input ,unable to generate star index folder
0
gravatar for manasa22.reddy
2.0 years ago by
United States
manasa22.reddy40 wrote:

Hi everyone ,

Iam 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

rna-seq tool • 839 views
ADD COMMENTlink modified 24 months ago by darbinator230 • written 2.0 years ago by manasa22.reddy40

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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Furthermore, you posted this as a "Tool", a post type which is intended to announce new tools. I have converted it to a Question.

ADD REPLYlink written 2.0 years ago by WouterDeCoster45k

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

ADD REPLYlink modified 24 months ago • written 24 months ago by darbinator230
1
gravatar for Eric Lim
2.0 years ago by
Eric Lim1.7k
Stoke Therapeutics, Inc
Eric Lim1.7k wrote:

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/

ADD COMMENTlink written 2.0 years ago by Eric Lim1.7k
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