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mlbendall / telescope

Quantification of transposable element expression using RNA-seq
MIT License
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index.gtf file issue (loci column and file format) #36

Open jamesc99 opened 2 years ago

jamesc99 commented 2 years ago

Hi,

Thanks for developing this tool. and I have two questions about the gtf annotation file that required by telescope

  1. how to generate the file format like you provide in the sample directory? I couldn't find such a format online.
  2. how to add loci column in the annotation file? I have run telescope several times with my data and it always returns the warning below. do you provide any script to generate required input annotation file? missing attribute "locus" (from __init__ in _annotation_intervaltree.py:45)

any suggestion would be highly appreciated! thanks

Ryan

CWYuan08 commented 1 year ago

Hi @jamesc99, did you manage to resolve this problem? I have the same issue... Thank you!

Kat-th-Liu commented 4 months ago

This has loci annotation https://github.com/mlbendall/telescope_annotation_db/tree/master/builds/retro.hg38.v1