the first line "Gene" is NM_003641|NA|chr11|+ ,which lost ‘genename’

Identification of APA sites from RNA-seq data

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the first line "Gene" is NM_003641|NA|chr11|+ ,which lost ‘genename’

Forum: General Discussion

Creator: Haifeng Sun

Created: 2018-07-16

Updated: 2018-07-16

Haifeng Sun - 2018-07-16

Gene
NM_003641|NA|chr11|+
NM_002391|NA|chr11|+
NM_001184740|NA|chr11|+
NM_001134774|NA|chr11|+
NM_001134775|NA|chr11|+

Dear:
The result is as beyond , use your example data is also the result .
But i want to have 'NA' become ”genename“ such as Ythdc2 and so on.
I think it's the "hg19.genemodel.bed" have some error ,but i don't know haow to get the right .bed file ?
Thanks very much if u can reply me !

Haifeng Sun
Email:haifeng4432@gmail.com
Nanjing Medical University

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Congting Ye - 2018-07-16
  
  Hi Haifeng,
  
  There is no error in the gene model file 'hg19.genemodel.bed'. The 'NA' is caused from that you did not provide a gene symbol file in the step of identifyDistal3UTR using parameter '-s'. The content of a gene symbol file should be like as follows,
  
  gene_id gene_name
  
  NM_001198993 NADK
  NM_017900 AURKAIP1
  NM_001014980 FAM132A
  NM_001198994 NADK
  NM_003820 TNFRSF14
  NM_003036 SKI
  NM_001242672 TTC34
  NM_152492 CCDC27
  
  Thanks for your interest in APAtrap!
  
  Congting Ye
  
  hg19.gene_symbol.txt
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

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