How to extract transcripts from Txdb with length >100
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@alexandrgopanenko-11598
Last seen 7 days ago
Germany

Hello!

1)I have created TxDb  using makeTxDbFromGFF.

2)Then I want to extract only transcript with length >100.

3)Then I want to export.gff3 to save a new gff3 file utilizing rtracklayer. 

 

How to do the second step with length parameter???

 

Thank you in advance,

Alex

genomicfeatures rtracklayer • 644 views
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@martin-morgan-1513
Last seen 7 days ago
United States

Extract the transcripts from the TxDb and subset for the width you are interested in

> tx = transcripts(TxDb.Hsapiens.UCSC.hg38.knownGene)
> length(tx)
[1] 197782
> tx100 = tx[width(tx) > 100]
> length(tx100)
[1] 192874

 

 

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Thank you very much!

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