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How to subset a UCSC table

I downloaded ensGene.txt file from UCSC here and wanted to create custom GFF annotation for MISO. I can generate the GFF annotation using the entire ensGene.txt file but I am only interested to generate for a small subset. Then I create a subset by grep such like:

$grep ENSG00000141510 ensGene.txt > ensGens_sub.txt

But I got error when I rerun the rnaseqlib program:

    Making GFF alternative events annotation...
  - UCSC tables read from: /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local
  - Output dir: /data/projects/JingChen-TCGA/Alternative_splicing/Data/miso_annotation/tp53
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/rnaseqlib/gff/gff_make_annotation.py", line 65, in <module>
    main()
  File "/usr/local/lib/python2.7/dist-packages/rnaseqlib/gff/gff_make_annotation.py", line 61, in main
    make_annotation(args)
  File "/usr/local/lib/python2.7/dist-packages/rnaseqlib/gff/gff_make_annotation.py", line 29, in make_annotation
    raise Exception, "No UCSC tables found in %s." %(tables_dir)
Exception: No UCSC tables found in /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local.

It says "No UCSC tables found in /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local.".

Does anybody know the reasons and how to correctly subset the UCSC table like ensGene.txt?

assembly
• 2,664 views • link
written by ddzhangzz ddzhangzz

Did you make sure the table you are using as input for your program is present at /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local ?

do following and check

ls /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local
• 0 views • link
written by venu venu 
$ ll /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local
total 8
-rw-r--r-- 1 3849 Jun  8 14:20 TP53-ensGene.txt
-rw-r--r-- 1 4015 Jun  8 11:21 TP53-Homo_sapiens_Transcript_Summary.txt
• 0 views • link
written by ddzhangzz ddzhangzz

1 answer

rename TP53-ensGene.txt to ensGene.txt and try one more time. As I understand from the MISO link you provided it seems the program is searching for ensGene.txt by default.

• 0 views • link
written by venu venu

Thanks! It works. Never thought it was caused by name...:(.

• 0 views • link
written by ddzhangzz ddzhangzz

Great. I'm moving my comment to answer. Please feel free to mark it accepted so the question will be closed and future users will find correct answer instead of searching in comments.

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written by venu venu

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