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Some problem when using its package #2

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yuanlizhanshi opened this issue Sep 7, 2022 · 4 comments
Open

Some problem when using its package #2

yuanlizhanshi opened this issue Sep 7, 2022 · 4 comments

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@yuanlizhanshi
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  1. when I load my bigwig file, it only works on my current work directory， such as :
    loadBigWig('../bigwig/my.bigwig')
    and get:
    Error in $<-.data.frame(*tmp*, "fileName", value = c("..", "/my"))

  2. The import gtf function is comes from rtracklayer, but you did not mention it, which took me a while to find it.
@yuanlizhanshi
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3.trancriptVis function may take gene_name column in gtf to find the gene, but in many gtf file, it did not have gene_name column, replaced it with gene_id

@junjunlab
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loadBigWig has been fixed. trancriptVis does not support NCBI gtf file, please using gtf from UCSC, ENSEMBL or GENCODE database.

@yuanlizhanshi
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loadBigWig has been fixed. trancriptVis does not support NCBI gtf file, please using gtf from UCSC, ENSEMBL or GENCODE database.

But your reference gtf is hg19.ncbiRefSeq.gtf, I think there are some problems in your function

@junjunlab
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hg19.ncbiRefSeq.gtf is just an example, gtf from UCSC, ENSEMBL or GENCODE also can be used as trancriptVis input.

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@yuanlizhanshi @junjunlab