RNAseq analysis of organism not included in BSgenome using QuasR
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@anuranjansrathore-24376
Last seen 15 months ago

Hello,

I am new to QuasR and trying to analyse RNASeq data of Tomato plant, whose genome has not been included in the package. Kindly guide me as to how to proceed with the transcriptome analysis of organisms not included here.

Thank you

Anuranjan

QuasR • 225 views
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@michael-stadler-5887
Last seen 22 days ago
Switzerland

Hi Anuranjan

It's no problem to use QuasR for an organism for which there is no BSgenome package available. In that case, you can use a genome reference in the form of a fasta file (see for example the code in section 3.2 of the vignette, or also the documentation in ?qAlign). In your qAlign call, you then refer to that fasta file, e.g. for RNA-seq data you could:

proj <- qAlign("sample_file.txt", "/path/to/my/reference/genome.fa",
               splicedAlignment = TRUE, aligner = "Rhisat2")

and you can also use the clObj argument to enable parallel processing. An alignment index for the genome will automatically created in the same folder containing genome.fa, so make sure you have write permission to that folder.

Best wishes, Michael

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