Use an annotated transcript in STAR but no .gtf file available
1
0
Entering edit mode
17 months ago
luzglongoria ▴ 50

Hi there,

I'm going to start with my RNA-seq analyses using STAR for mapping. I have no reference genome perse , what I have is an annotated transcript from a previous study. I made this annotated transcript by using Trinity (de novo assembling) and I wonder if it is possible to run STAR with this Trinity file as a reference genome.

This Trinity file is annotated but I don't have a .GFT file to include in the Genome Indexing Parameters for STAR. I know this option is only used for –runMode genomeGenerate but it's going to be the first time for me and I'm not sure how to do it.

I just run my read in a normal way with this Trinity file or I should do some thing before?

Any help is more than welcome.

Best,

Luz

gtf RNA-seq STAR • 982 views
ADD COMMENT
2
Entering edit mode
17 months ago
Dave Carlson ★ 1.8k

STAR is a spice-aware aligner that is designed for mapping to a genome assembly, not a transcriptome.

If all you have is the transcriptome assembly, I would recommend using a different tool, depending on what your downstream goals are. For example, you could use RSEM for mapping + quantification. Or Salmon or Kallisto for quantification.

Trinity comes with several scripts that make this process easier. See the following:

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification

ADD COMMENT
0
Entering edit mode

Thank you so much for your answer.

My goal if to filter my dataset since I’m working with parasites infecting another organism (mix reads). I would like to use this transcriptome assembly in order to filter and then (and after other filtering process) quantify with Trinity tools , as you suggested.

Maybe I could use other tools as Hisat2?

ADD REPLY
1
Entering edit mode

I believe Hisat2 is also designed for mapping RNA-Seq reads to a genome instead of a transcriptome. However, if you use RSEM, you can map your reads to your transcriptome assembly using bowtie2.

ADD REPLY
0
Entering edit mode

Great ! Thank you so much.

ADD REPLY

Login before adding your answer.

Traffic: 2825 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6