How can I use Darts_DNN for data mapped to hg38? #8

evachengzi · 2019-07-12T09:46:58Z

No description provided.

zj-zhang · 2019-07-21T20:30:30Z

Hi @evachengzi
Because the sequence features are built for hg19, the exon coordinates should map to the hg19 genome assembly. Please convert the hg38 coordinates in DARTS_BHT output file to hg19 using UCSC liftOver:
https://bioconda.github.io/recipes/ucsc-liftover/README.html

The detailed steps are below:

run Darts_BHT on the bam files to generate the "darts_bht.flat.out.txt" output.
use liftOver to convert coordinates in the above output file to hg19, e.g. the output is "darts_bht.converted_hg19.txt"
run Darts_DNN on the converted hg19 file "darts_bht.converted_hg19.txt".

evachengzi · 2019-07-22T07:56:24Z

Thank you for your detailed explanation！

I have converted the exon coordinates in the "ID" column of "darts_bht.flat.out.txt" and run Darts_DNN on the converted hg19 file. But I still get the index error like the picture show. It seems like that there are only a few coordinates not in the resource of Darts_DNN?
And I found some coordinates that not mapped to hg19 when I convert them from hg38 to hg19. Liftover divided these coordinates to another file named "unmapped.bed". How would I deal with these unmapped coordinates in splicing ID ?
Looking forward to your reply！

YangpingLi · 2020-10-21T02:48:32Z

Do we have a sequence features built for hg38 now? This should be very useful!

Thanks!

zj-zhang · 2020-10-21T03:55:36Z

Ping @zcpan on this issue

zcpan · 2020-10-23T01:28:23Z

Hi @YangpingLi ,
Thanks for your interest in DARTS. We currently do not have a plan to make hg38-version feature sets, but it is definitely on our to-do list. We will let you know once we have the feature sets. Thanks!

yangjywhu · 2020-12-15T03:51:56Z

I have converted the exon coordinates in the "ID" column of "darts_bht.flat.out.txt" and run Darts_DNN on the converted hg19 file. But I still get the index error like the picture show. It seems like that there are only a few coordinates not in the resource of Darts_DNN?

@evachengzi I don't know how to do it :( How did you convert the coordinates? Thank you! Look forward to your reply.

astulaaa · 2022-09-19T07:39:54Z

Hello, since a couple of years passed, are there any updates on accommodating hg38-aligned genomes or we still need to use lift-over to convert flat file to hg19 coordinates? https://darts-dnn.readthedocs.io/en/latest/ still mentions conversion.

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How can I use Darts_DNN for data mapped to hg38? #8

How can I use Darts_DNN for data mapped to hg38? #8

How can I use Darts_DNN for data mapped to hg38? #8

How can I use Darts_DNN for data mapped to hg38? #8

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