# Genome index STAR

**URL:** <https://help.galaxyproject.org/t/genome-index-star/13220>\
**Category:** Uncategorized\
**Tags:** transcriptomics, igv\
**Created:** [August 13, 2024, 2:17pm UTC](https://help.galaxyproject.org/t/genome-index-star/13220 "2024-08-13T14:17:39Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![CARTAS\_ESPINEL\_IRENE](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/cartas_espinel_irene/32/5939_2.png) [@CARTAS\_ESPINEL\_IRENE](https://help.galaxyproject.org/u/CARTAS_ESPINEL_IRENE)\
**Post date:** [August 13, 2024, 2:17pm UTC](https://help.galaxyproject.org/t/genome-index-star/13220/1 "2024-08-13T14:17:39Z")

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Hello, i would like to built my genome index to use STAR but i want to use a fasta with the cDNAs like this one “Mus\_musculus.GRCm38.cdna.all.fa” so the option " --genomeFastaFiles /Mus\_musculus.GRCm38.cdna.all.fa". I guess i do not need the option “–SjdbGTFile”. I want to do this because i want the reads that align to exons-genes to be align and recover the unmapped reads for further analyisis. Is this possible? what should i do? thank you very much

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [August 13, 2024, 7:15pm UTC](https://help.galaxyproject.org/t/genome-index-star/13220/2 "2024-08-13T19:15:48Z")

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Welcome, @CARTAS_ESPINEL_IRENE

Are you running the tool in Galaxy?

If yes, and working at a public server, see this topic from earlier today for how to use the Custom Genome and Custom Build functions (any tool). Please see [Bowtie2 brucella reference - #2 by jennaj](https://help.galaxyproject.org/t/bowtie2-brucella-reference/13214/2).

If yes, and working on your own local server, we happened to have another topic today, and that answer will also apply to this use case. Please see [STAR --genomeDir option - #2 by jennaj](https://help.galaxyproject.org/t/star-genomedir-option/13216/2).

With that context, for your question here

> [@CARTAS\_ESPINEL\_IRENE](#):
>
> i want to use a fasta with the cDNAs like this one “Mus\_musculus.GRCm38.cdna.all.fa” so the option " --genomeFastaFiles /Mus\_musculus.GRCm38.cdna.all.fa". I guess i do not need the option “–SjdbGTFile”. I want to do this because i want the reads that align to exons-genes to be align and recover the unmapped reads for further analyisis. Is this possible? what should i do?

Wherever you are running RNA STAR, if you want to filter reads based on matches (or non-matches) to exon genomic footprints

- when aligning to a _reference genome_, you will need to inform the tool about _where_ those exons are located (the coordinates). The reference annotation is how you do that.
- when aligning to a _reference transcriptome_, then you have already filtered out the non-transcript regions.

You could test this out: align with the annotation and without, to the transcriptome versus genome. Then examine the BAMs and reference annotation in a genome browser like UCSC or IGV. Then review: where are the reads aligning? Are you including or excluding mapped reads as expected? Then tune parameters, and rerun, until you get the desired result.

Hope this helps! 🙂