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using a non-standard mouse genome build #37
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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 |

# 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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Hi, The attachment is missing. Could you please tray again? |
Here is the gtf. (it was rejected because not a recognized file type). |
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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.
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