Uploading new reference genome

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Hi all,

I want to add a reference genome for RNA-seq analysis to use on HISAT2 and FeatureCounts.

Genome assembly ARS-UI_Ramb_v2.0

How do I go about doing this and what file formats do the they need to be for each program?

Thanks in advance.

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Hi @Maxmus
Upload FASTA file into your history and while composing HiSAT2 job, change source of genome from built-in to ‘in your history’.
Hope that helps.
Kind regards,
Igor

3

Hi @igor ,

Thanks for your reply. Yes the FASTA file works to align to the genome using HISAT2, however, this does not work when using ‘FeatureCounts’. I have tried changing the file format to GTF but that doesn’t count any genes. Do I need to download an annotation file or build a custom genome to conduct FeatureCounts?

Many thanks,
Max

4

Hi @Maxmus yes, you need a gene annotation file. Usually annotation files are available from the same source, as genome assembly. During setup of featureCounts job change Gene annotation file to ‘in your history’. Make sure the gene annotation is for the assembly used for read mapping. Inspect the gene annotation file and double check that values used for read counting are present in the file. By default, reads are counted against exons and aggregated for gene_id attribute - see Advanced options in featureCounts.
Kind regards,
Igor

1 Like
5

Hi @igor ,

Many thanks for your help, this worked a charm!

Best,
Max