search

vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
78 stars 29 forks source link

How to call vast-tools align with Dre #64

Closed alicezyj1 closed 6 years ago

alicezyj1 commented 6 years ago

Hi there,

This is just a question about how to use the new version of vast-tools/3.1.0 to analyze zebrafish RNA-seq data. I used the original version of vast-tools to analyze human data by calling: vast-tools align file_1.fastq.gz file_2.fastq.gz --sp Hsa -c 32 --expr There are three options for --sp Hsa/Mmu/Gga I downloaded the new version of vast-tools which supports the analysis of zebrafish and sea urchin RNA-seq data. But there are still the original three options for --sp. I am wondering if there is any other way to write this command for analysis of zebrafish data?

Many thanks!

mirimia commented 6 years ago

Hey,

Sorry, the help text wasn't updated. It takes any of the available species (I changed it to --sp Hsa/Mmu/etc).

You can run vast-tools already for zebrafish using --sp Dre.

Cheers Manu