RNAseq analysis: how to add new gene into an existing worm based reference

Question

[leranwangcs]

Hi,

I downloaded the worm based gene reference database from biomart for RNAseq analysis. Now I'm trying to add one more gene in to the reference based on my interest of research, but could not find a tutorial of how to do this.

Anyone has any idea or experience on this?

Thanks!

Leran

[GenoMax]

Unless I am misinterpreting your question.

Now I'm trying to add one more gene in to the reference based on my interest of research

You could add it as an extra chromosome (or an extra transcript) by editing the file or simply doing cat genome.fa gene_added.fa > new_genome.fa (assuming your gene sequence is in fasta format in the gene_added.fa file).

[Haci]

If you would like to obtain counts corresponding to your "new gene(s)", you will have to edit your annotation file as well.

Answer 1

[jkim]

This is from 10x website for cell ranger to make a custom reference but i think it probably should work for RNAseq aligners.

Add marker gene to a fa and gtf

[leranwangcs]

Thank you!! It worked very well!

Answer 2

[ahmad mousavi]

Hello,

if you mean adding new known genes to the reference genome/transcriptome then mapping, you should doing some code such as :

cat reference_genome.fa  some_new_genes.fa > new_reference_genome.fa

Then index the new genome file and map the samples to it, you need to change the GTF / gff3 file as well.

[leranwangcs]

Thank you! I used this code for modifying the .fa file!