Problem with introns numerotation on negative strand in bed output files

[MOUREN Jean christophe]

Hello,

I've noticed that the numerotation of introns on the negative strand in the output bed files is not set the same way as the exons bed files : what is marked as the last intron should be annoted as the first intron and vice versa.

Here's an output example of the intron and exons bedfiles for comparaison :

Introns bed file :

chr1    1311924 1312017 ENST00000540437.5_intron_0_0_chr1_1311925_r     0       -
chr1    1312147 1312225 ENST00000540437.5_intron_1_0_chr1_1312148_r     0       -
chr1    1312368 1312439 ENST00000540437.5_intron_2_0_chr1_1312369_r     0       -

Exons bed file :

chr1    1311858 1311924 ENST00000540437.5_cds_18_0_chr1_1311859_r       0       -
chr1    1312017 1312147 ENST00000540437.5_cds_17_0_chr1_1312018_r       0       -
chr1    1312225 1312368 ENST00000540437.5_cds_16_0_chr1_1312226_r       0       -

Respectfully,

Jean-Christophe Mouren

Phd student, TAGC laboratory | U1090 INSERM

Aix-Marseille Université

[Gerardo Perez]

Hello, Jean-Christophe.

Thank you for your interest in the Genome Browser and for reporting your issue.

We were able to replicate your issue and have created an internal ticket to fix the intron BED output for the negative strand on the Table Browser. Unfortunately, we cannot provide an estimated release date for the fix.

Thank you again for bringing this to our attention. If you would like email updates about the UCSC Genome Browser, you can subscribe to our Announcements Mailing List:

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Gerardo Perez
UCSC Genomics Institute

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[Gerardo Perez]

Hello, Jean-Christophe.

We have fixed the intron BED output for the negative strand on the Table Browser. Let us know if you run into any more issues when using the UCSC Genome Browser.

Thank you again for bringing this issue to our attention.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

[Benoit Ballester]

Dear Gerardo, 

Thanks for fixing the Intron numeration on the negative strand (which was the same issue spotted a few month back for the exon).

Quick question : 

Next to the exon/intron number, what does the “0” mean (in bold red)?

Shouldn’t it be the total number of exons/introns in that transcript ?

Hence, it is always set to 0. 

Could you give us some information on that ? 

Thanks, 

Introns bed file :

chr1    1311924 1312017 ENST00000540437.5_intron_0_0_chr1_1311925_r     0       -
chr1    1312147 1312225 ENST00000540437.5_intron_1_0_chr1_1312148_r     0       -

chr1    1312368 1312439 ENST00000540437.5_intron_2_0_chr1_1312369_r     0       -

Exons bed file :

chr1    1311858 1311924 ENST00000540437.5_cds_18_0_chr1_1311859_r       0       -

chr1    1312017 1312147 ENST00000540437.5_cds_17_0_chr1_1312018_r       0       -

chr1    1312225 1312368 ENST00000540437.5_cds_16_0_chr1_1312226_r       0       -

Cheers, 

Ben

--
Benoît Ballester, PhD
INSERM U1090 TAGC
Aix-Marseille-Université
Parc Scientifique de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr

ReMap2022: http://remap.univ-amu.fr/ 

[Gerardo Perez]

Hello, Benoit,

Thank you for your interest in the Genome Browser and for sending your inquiry.

The bolded “0” that you shared indicates there are no extra bases included around the exon or intron. You can configure this setting by adding a plus number of bases for exons or introns on the Output BED settings page:

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/9E191C60-0DD0-463A-95E2-B8C146466965%40inserm.fr.