About Darts_DNN build_feature error

[liyangyang12]

when I build feature using -e parameter,it occurs error information

my kallisto result

Looking forward to your help !

[zj-zhang]

For human data, the current transcript to gene mapping uses GENCODE v19 for the hg19 assembly:
https://www.gencodegenes.org/human/release_19.html
For now, please use GENCODE file to build the Kallisto Index from the above link to run DARTS DNN.
Kindly note that DARTS DNN is only trained for human; it does not work on mouse data.

[liyangyang12]

Thank you very much! By the way, how can I use DARTS DNN on mouse data? Does "Darts_DNN train " works?
And I have another question about Darts_DNN build feature, what kind of data do we need to provide to use parameter --cis-feature ? and Is it legal to omit parameters --cis-feature ?
Looking forward to your help!

[zj-zhang]

In fact, these two issues are related. Currently we cannot train mouse model because 1) we do not have the compiled mouse cis-features; 2) we do not have compiled large scale training data for mouse.
In using build_feature, if no --cis-feature is provided, DARTS will find the downloaded cis-features by default. Check the "get_data" module for more details on how to download cis-features:
https://darts-dnn.readthedocs.io/en/latest/get_started.html#using-predict

[liyangyang12]

Ok, I see.
Thanks again for your patience !

[kyrenexu]

I use GENCODE file(ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/gencode.v31.pc_transcripts.fa.gz) to build the Kallisto Index，but still occurs similar error information

[kyrenexu]

This is my kallisto quant result

Looking forward to your help !Thank you!

[zj-zhang]

Hi @kyrenexu
We are currently working on an implementation to deal with different GTF file versions. Please stay tuned.
For now, please use the gencode V19 as GTF file (instead of V31) when running kallisto:
https://www.gencodegenes.org/human/release_19.html

[kyrenexu]

It works!Thank you so much!