User: genecats.ucsc
genecats.ucsc • 560
- Reputation:
- 560
- Status:
- Trusted
- Location:
- Last seen:
- 2 months, 1 week ago
- Joined:
- 2 years, 2 months ago
- Email:
- g************@gmail.com
Please know UCSC supports several lists where users can email questions and search archived answers:
-For posting general non-mirror and non-confidential questions: * Post to the Public Help Forum: Email genome@soe.ucsc.edu or Search the Public Archives: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome
-For posting mirror-specific questions: * Post to the Mirror Help Forum: Email genome-mirror@soe.ucsc.edu or Search the Mirror Archives : https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror
-For posting questions with information that is private/confidential: * Email genome-www@soe.ucsc.edu
Posts by genecats.ucsc
<prev
• 53 results •
page 1 of 6 •
next >
0
votes
1
answer
160
views
1
answers
... Add exonNumbers="off" to your track line. ...
written 10 weeks ago by
genecats.ucsc • 560
3
votes
1
answer
189
views
1
answers
... 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 4 months ago by
genecats.ucsc • 560
1
vote
1
answer
287
views
1
answers
... 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 4 months ago by
genecats.ucsc • 560
0
votes
1
answer
563
views
1
answers
... Did this work for hg19 as well? ...
written 5 months ago by
genecats.ucsc • 560
1
vote
1
answer
563
views
1
answers
... 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 5 months ago by
genecats.ucsc • 560
0
votes
1
answer
563
views
1
answers
... 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 5 months ago by
genecats.ucsc • 560
0
votes
1
answer
385
views
1
answers
... 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 9 months ago by
genecats.ucsc • 560
0
votes
1
answer
385
views
1
answers
... 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 10 months ago by
genecats.ucsc • 560
1
vote
1
answer
266
views
1
answers
... 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 10 months ago by
genecats.ucsc • 560
1
vote
2
answers
498
views
2
answers
... 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 10 months ago by
genecats.ucsc • 560
Latest awards to genecats.ucsc
Scholar
4 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
10 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Supporter
10 months ago,
voted at least 25 times.
Scholar
12 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Scholar
13 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
16 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Scholar
17 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Scholar
19 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
21 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
22 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Autobiographer
2.2 years ago,
has more than 80 characters in the information field of the user's profile.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 951 users visited in the last hour