hg19 refseq genes standard bed file
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Sarah Halawa
May 24, 2017, 8:33:54 PM5/24/17
to gen...@soe.ucsc.edu
Dear concerned Sir/Madame
I followed these steps to get the hg19 annotation file
I followed these steps to get the hg19 annotation file
- I went to the UCSC genome browser
- Selected "Genes and Gene prediction tracks" from the "group" drop-down menu.
- Selected the "Refseq Genes" from the "track" drop-down menu.
- Selected "refGene" table
- Selected "BED- browser extensible data" for the "output format".
- Clicked "get output" and on the following page clicked "get BED"without changing any options.
- Finally I saved the output as a text file
Unfortunately, it didn't give the expected result.
Is there a standard refseq.hg19.bed.txt file?
Thank you so much!
All the best,
Sarah
Cath Tyner
May 26, 2017, 8:14:31 PM5/26/17
to Sarah Halawa, UCSC Genome Browser Public Help Forum
Hi Sarah,
Thank you for contacting the UCSC Genome Browser support team and inquiring about finding the nearest genes based on a reference point, including the distance from the reference point to the transcript, as well as the strand.
Please see this recently revised wiki page:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes
If you are comfortable creating a script, you can copy the script in this section and create a script:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes#Script_for_refGene_on_hg19
This script uses your example as reference point: chr1 991973 991973
and finds the 10 nearest transcripts in refGene, hg19, that are upstream (and the 10 nearest downstream).
The output includes the transcript name and coords, the gene name/alias, the strand, and the distance (in bp) from the reference point to each transcript.
Please note that there is a url to a genome browser session in the section for "refGene/hg19" which visualizes the example output.
Please also note the section for "Alternatives" which point to other options to accomplish your goal.
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes#Alternatives
* Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu
Thank you for contacting the UCSC Genome Browser support team and inquiring about finding the nearest genes based on a reference point, including the distance from the reference point to the transcript, as well as the strand.
Please see this recently revised wiki page:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes
If you are comfortable creating a script, you can copy the script in this section and create a script:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes#Script_for_refGene_on_hg19
This script uses your example as reference point: chr1 991973 991973
and finds the 10 nearest transcripts in refGene, hg19, that are upstream (and the 10 nearest downstream).
The output includes the transcript name and coords, the gene name/alias, the strand, and the distance (in bp) from the reference point to each transcript.
Please note that there is a url to a genome browser session in the section for "refGene/hg19" which visualizes the example output.
Please also note the section for "Alternatives" which point to other options to accomplish your goal.
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes#Alternatives
Please respond to this list if you have further questions!
Thank you for contacting the UCSC Genome Browser support team.
Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:
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Cath
. . .
Cath Tyner. . .
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute--
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Sarah Halawa
Jun 7, 2017, 11:38:58 AM6/7/17
to Cath Tyner, UCSC Genome Browser Public Help Forum
Hey Cathy,
Hope you're doing great!chr20 33506636 33563217 MYH7 0 + 33513606 33562869 0 35 350,71,123,289,57,83,166,107,252,97,102,159,179,183,145,147,231,194,128,170,168,135,144,134,139,349,122,121,122,2616,114,156,102,57,612, 0,2902,4580,6867,8177,10345,10641,11568,11906,14492,16652,17275,17976,18472,20104,21051,22473,23833,24248,24578,35240,35815,38033,39128,41183,42325,43201,44655,46449,46995,52344,52641,53549,54604,55969,
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Christopher Lee
Jun 13, 2017, 1:00:25 PM6/13/17
to Sarah Halawa, Cath Tyner, UCSC Genome Browser Public Help Forum
Hi Sarah,
Thank you for your questions about obtaining a bed file of transcripts
nearest to a particular position, and obtaining a bed file of
transcripts with an official gene symbol in the 4th column.
As for your second question, there is no way to get a bed file with
the gene symbol as the 4th field from the Table Browser. However you
could get that info from our public MySQL server. You will need to
install MySQL and have access to a command line, where you can run the
following command:
$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -Ne "select
chrom, txStart, txEnd,\
name2, score, strand, cdsStart, cdsEnd, 0 as itemRgb, exonCount,
exonStarts, exonEnds \
from refGene" hg19 > hg19.refGeneTranscripts.bed
This will result in a bed file of ALL hg19 refGene transcripts with
the name2 field as the 4th column.
As for finding the transcript, distance, etc., nearest to a single
position, this also cannot be accomplished via the Table Browser, but
can be accomplished via the script from the wiki page in Cath's
previous answer. Where are you struggling in trying to run the script,
perhaps we can help you get it going so you can keep using it in the
future?
Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
>> * Subscribe: Email genome-annou...@soe.ucsc.edu
>> * Unsubscribe: Email genome-announ...@soe.ucsc.edu
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Thank you for your questions about obtaining a bed file of transcripts
nearest to a particular position, and obtaining a bed file of
transcripts with an official gene symbol in the 4th column.
As for your second question, there is no way to get a bed file with
the gene symbol as the 4th field from the Table Browser. However you
could get that info from our public MySQL server. You will need to
install MySQL and have access to a command line, where you can run the
following command:
$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -Ne "select
chrom, txStart, txEnd,\
name2, score, strand, cdsStart, cdsEnd, 0 as itemRgb, exonCount,
exonStarts, exonEnds \
from refGene" hg19 > hg19.refGeneTranscripts.bed
This will result in a bed file of ALL hg19 refGene transcripts with
the name2 field as the 4th column.
As for finding the transcript, distance, etc., nearest to a single
position, this also cannot be accomplished via the Table Browser, but
can be accomplished via the script from the wiki page in Cath's
previous answer. Where are you struggling in trying to run the script,
perhaps we can help you get it going so you can keep using it in the
future?
Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
>> * Unsubscribe: Email genome-announ...@soe.ucsc.edu
Sarah Halawa
Jun 19, 2017, 11:41:31 AM6/19/17
to Christopher Lee, Cath Tyner, UCSC Genome Browser Public Help Forum
Hey Christopher,
Can't thank you enough! This was of tremendous help:)
Thank you very much
Best wishes,
Sarah
Can't thank you enough! This was of tremendous help:)
Thank you very much
Best wishes,
Sarah
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