using a non-standard mouse genome build

[jcm6t]

Is there a way to pass in a non-custom genome build in the read_coldata() step ? My reads are aligned to a specific mouse strain genome but it is not the standard mm build.

Thanks.

[PoisonAlien]

Hi,

build argument is only useful if you'd like to query UCSC for gene models. In your case, you should use a custom gtf file. Also set query_ucsc = FALSE so that it wont try to connect to the UCSC.

[jcm6t]



implemented as suggested:

t <- track_extract(colData = bigwigs, query_ucsc = FALSE, gtf=gtffile, gene = "Kirrel2")

but received error:

Parsing gtf file.. Error in track_extract(colData = bigwigs, query_ucsc = FALSE, gtf = gtffile, : No transcript models found for Kirrel2

I have attached the gtf.

Trying to debug:

etbl = .parse_gtf(gtf = "kirrel2.gtf", genename = "Kirrel2") Parsing gtf file.. Warning message: In .parse_gtf(gtf = "kirrel2.gtf", genename = "Kirrel2") : Requested gene or transcript could not be found within the requested loci!

Which is a bit strange since the gtf is formatted correctly and parsed by trackplot.R and Kirrel2 is specified as a gene_name in the parsed info column. I thought you would be able to see the problem faster.

Thanks, Joe

On Jun 30, 2024, at 4:31 AM, Anand Mayakonda @.***> wrote:

Hi,

build argument is only useful if you'd like to query UCSC for gene models. In your case, you should use a custom gtf file. Also set query_ucsc = FALSE so that it wont try to connect to the UCSC.

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[PoisonAlien]

Hi,

The attachment is missing. Could you please tray again?

[jcm6t]

kirrel2.gtf.txt

Here is the gtf. (it was rejected because not a recognized file type).