bed file questions

[Hong Chen]

Hi,

 

I use the UCSC table brower below to generate bed files for a list of genes. I have two questions:

 

1, are the bed file generated based on all transcripts of genes, or the major or longest transcripts?

2, if I choose ‘genome’ for region, I cannot generate the bed file for the genes below for example (mitochondria genes etc. ). Is there any way to generate bed files for those genes?  Thank you.

MT-CO1

ODAD1

TAFAZZIN

 

 

 

Hong

[Gerardo Perez]

Hello, Hong.

Thank you for your interest in the Genome Browser and for your questions about the Table Browser BED output.

We will address your questions below:

1, are the bed file generated based on all transcripts of genes, or the major or longest transcripts?

The BED output on transcripts will depend on the table selected for the dataset. For example, the RefSeq Select table from the NCBI RefSeq dataset will have one transcript per gene based on criteria (https://www.ncbi.nlm.nih.gov/refseq/refseq_select/) and the BED output will be the one transcript. Where the RefSeq All, RefSeq Curated, and UCSC RefSeq tables can have multiple transcripts and will output multiple transcripts in BED output. You may find the following FAQ entry helpful: https://genome.ucsc.edu/FAQ/FAQgenes.html#singledownload

2, if I choose ‘genome’ for region, I cannot generate the bed file for the genes below for example (mitochondria genes etc. ). Is there any way to generate bed files for those genes? Thank you.

MT-CO1
ODAD1
TAFAZZIN

We see from the image you shared that you are interested in using the UCSC RefSeq (refGene) dataset for hg19. Unfortunately, the MT-CO1 does not exist in refGene, but exists as COX1 (https://www.genecards.org/cgi-bin/carddisp.pl?gene=MT-CO1) in the ncbiRefSeqOther dataset. As for the other two, you can use refGene but will have to use different names:
ODAD1 -> CCDC114 (https://www.genecards.org/cgi-bin/carddisp.pl?gene=ODAD1)
TAFAZZIN -> TAZ (https://www.genecards.org/cgi-bin/carddisp.pl?gene=TAFAZZIN)

You can paste these gene identifiers by clicking the identifiers (names/accessions) paste list option on the Table Browser, then set the output format to BED to generate a BED file.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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