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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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I found some bugs in the refGene.txt #225

Open yang050036 opened 11 months ago

yang050036 commented 11 months ago

Hi, Thanks for you great software. But I found some error in the refGene.txt. For exomple, I fount the information of 'NOTCH2NLC' have error in start and end column: 211 NM_001364013 chr1 + 145209159 145283180 145209308 145282031 7 145209159,145209323,145209379,145248820,145273184,145281368,145281954, 145209323,145209377,145209436,145248894,145273444,145281704,145283180, 0 NOTCH2NLC cmpl cmpl 0,0,0,0,2,1,1, 23 NM_001364012 chr1 - 120391203 120612242 120539288 120572566 9 120391203,120391253,120531874,120537165,120539357,120539619,120547951,120572528,120611947, 120391240,120391484,120537153,120539353,120539369,120539955,120548211,120572610,120612242, 0 NOTCH2NLC cmpl cmpl -1,-1,-1,1,1,1,2,0,-1, The second row is error, becase I found the range is belong to 'NOTCH2' but not 'NOTCH2NLC'. Any suggestion for me?

kaichop commented 11 months ago

This file is compiled by UCSC Genome Browser, based on refGene alignment to human genome. I am not sure what problem you are referring to, both rows are for a transcript that is named as NOTCH2NLC by refSeq.

On Sun, Jul 9, 2023 at 11:11 PM yang050036 @.***> wrote:

Hi, Thanks for you great software. But I found some error in the refGene.txt. For exomple, I fount the information of 'NOTCH2NLC' have error in start and end column: 211 NM_001364013 chr1 + 145209159 145283180 145209308 145282031 7 145209159,145209323,145209379,145248820,145273184,145281368,145281954, 145209323,145209377,145209436,145248894,145273444,145281704,145283180, 0 NOTCH2NLC cmpl cmpl 0,0,0,0,2,1,1, 23 NM_001364012 chr1 - 120391203 120612242 120539288 120572566 9 120391203,120391253,120531874,120537165,120539357,120539619,120547951,120572528,120611947, 120391240,120391484,120537153,120539353,120539369,120539955,120548211,120572610,120612242, 0 NOTCH2NLC cmpl cmpl -1,-1,-1,1,1,1,2,0,-1, The second row is error, becase I found the range is belong to 'NOTCH2' but not 'NOTCH2NLC'. Any suggestion for me?

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yang050036 commented 11 months ago

The start and end is 120391203 and 120612242 in scond row for NOTCH2NLC. But the range is belong to 'NOTCH2' in UCSC Genome Browser: image