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