User: genecats.ucsc
genecats.ucsc • 560
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Posts by genecats.ucsc
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... Hi m93,
I think there is some confusion here that arose from that genomewiki page you linked. BED data (and bigBed) is displayed in the UCSC Genome Browser as "blocks" along the genome, while wiggle data (and bigWig) is displayed as a signal (with a genomic base on the x axis and some value on the ...
written 5 days ago by
genecats.ucsc • 560
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... Yes this is correct. Also note that if your file is too large to be stored on Github, you can use the CyVerse Discovery Environment to host the file:
https://www.cyverse.org/
Cyverse might be a little easier since you should be able to upload a single directory of your hub data (including hub.txt a ...
written 14 days ago by
genecats.ucsc • 560
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... Did this work for hg19 as well? ...
written 7 weeks ago by
genecats.ucsc • 560
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... NCBI did not include predicted transcripts with their latest hg19 annotation, as stated here:
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/README_addendum.txt
Which is why they don't show up in our tables for hg19. I s ...
written 7 weeks ago by
genecats.ucsc • 560
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... The refGene table only contains NM and NR sequences from NCBI, which are then mapped onto the genome with BLAT. If you want all sequences, including the XM, XR, etc, you want to query the "ncbiRefSeq" table:
mysql -h genome-mysql.soe.ucsc.edu -ugenome -Ne "select name, name2 from ncbiRefSeq" hg ...
written 7 weeks ago by
genecats.ucsc • 560
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... Sorry for the late reply but yes that is correct. The problem here is the GTF output function from the Table Browser, there have been issues with that specific function for a long time.
If you want you can just download the rmsk table and work on it directly:
http://hgdownload.cse.ucsc.edu/goldenPa ...
written 5 months ago by
genecats.ucsc • 560
0
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... Here are the first few lines from the rmsk table for hg38, where I have filtered for items like "ERV24B":
#filter: (repName like 'ERV24B%')
#bin swScore milliDiv milliDel milliIns genoName genoStart genoEnd genoLeft strand repName repClass repFamily repStart repEnd repLeft id
675 1260 2 ...
written 5 months ago by
genecats.ucsc • 560
1
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... It is possible to generate those alignments with the pslPretty utility, available from our list of utilities:
http://hgdownload.soe.ucsc.edu/admin/exe
Here is an example where I also illustrate some other useful commands, faSomeRecords and pslSomeRecords, which are also available from the same dire ...
written 6 months ago by
genecats.ucsc • 560
1
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... Genomax already answered, but here is also a mysql command you can use if you don't want to download the entire hgcentral database dump:
$ mysql -h genome-mysql.soe.ucsc.edu -u genome -e "select name, scientificName from dbDb limit 5" hgcentral
+---------+----------------------------------- ...
written 6 months ago by
genecats.ucsc • 560
1
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... If you reset your cart (Genome Browser->Reset all user settings in the top blue menu bar) and then go back to the Genome Browser, when you shift+click, a dialog box should come up explaining different zooming and highlighting keyboard shortcuts as well as some highlighting options. There is also ...
written 6 months ago by
genecats.ucsc • 560
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