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Xinglab / DARTS

Deep-learning Augmented RNA-seq analysis of Transcript Splicing
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About Darts_DNN build_feature error #6

Open liyangyang12 opened 5 years ago

liyangyang12 commented 5 years ago

when I build feature using -e parameter,it occurs error information 图片 my kallisto result 图片 Looking forward to your help !

zj-zhang commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

Ok, I see. Thanks again for your patience !

kyrenexu commented 5 years ago

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 捕获

kyrenexu commented 5 years ago

This is my kallisto quant result 捕获 捕获 2

Looking forward to your help !Thank you!

zj-zhang commented 5 years ago

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 commented 5 years ago

It works!Thank you so much!