User: genecats.ucsc
genecats.ucsc • 500
- Reputation:
- 500
- Status:
- Trusted
- Location:
- Last seen:
- 2 weeks, 6 days ago
- Joined:
- 1 year, 5 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
• 47 results •
page 1 of 5 •
next >
0
votes
1
answer
84
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 20 days ago by
genecats.ucsc • 500
0
votes
1
answer
84
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 4 weeks ago by
genecats.ucsc • 500
1
vote
1
answer
88
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 4 weeks ago by
genecats.ucsc • 500
1
vote
2
answers
164
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 7 weeks ago by
genecats.ucsc • 500
1
vote
1
answer
150
views
1
answers
... 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 7 weeks ago by
genecats.ucsc • 500
1
vote
1
answer
125
views
1
answers
... As genomax said, you need to add a track definition line when you load your custom track, something like:
track type=bigWig name="Example Name" description="Example Description"
http://url.to.your/file
Here's a list of the different track types supported:
http://genome.ucsc.edu/goldenPath/ ...
written 8 weeks ago by
genecats.ucsc • 500
0
votes
1
answer
327
views
1
answers
... This error happens when you have wiggle lines like the following:
variableStep chrom=chromName span=5
1000 0.56
1001 0.55
In this case the positions 1000-1004 are supposed to have the value 0.56 but then on the next line positions 1001-1005 are supposed to have value 0.55, and since a ...
written 3 months ago by
genecats.ucsc • 500
1
vote
1
answer
327
views
1
answers
... Yes what are the other chrom lines like in the wiggle file though? Do all the chromosome names correspond to what is the chrom.sizes file? Try grepping for 'chr2' from your wiggle file and see what shows up. Or something like this to get only the chromosome names:
$ grep chrom userWig2.wig | c ...
written 3 months ago by
genecats.ucsc • 500
0
votes
1
answer
327
views
1
answers
... You need to make sure that all of the chromosome names in your wiggle file are accounted for in the chrom.sizes file.
For instance, if my wiggle file looks like this:
variableStep chrom=chr2CEN
3003560 0
And my chrom.sizes file looks like this:
chr2CEN 242193529
Then I can still run ...
written 3 months ago by
genecats.ucsc • 500
0
votes
2
answers
1.3k
views
2
answers
... Hi Samad,
wigToBigWig works fine for me with the following test wiggle file:
$ cat test.wig
variableStep chrom=chr1
3003560 0
3003561 0
3003562 0
3003563 0
$ wigToBigWig test.wig hg38.chrom.sizes out.bw
What commands are you running to generate a bigWig?
Additionall ...
written 3 months ago by
genecats.ucsc • 500
Latest awards to genecats.ucsc
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Supporter
8 weeks ago,
voted at least 25 times.
Scholar
3 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Scholar
4 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
7 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Scholar
8 months ago,
created an answer that has been accepted.
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
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Scholar
12 months ago,
created an answer that has been accepted.
For A: Batch download of hg19 sequences in bed file
Teacher
12 months ago,
created an answer with at least 3 up-votes.
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
13 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
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Batch download of hg19 sequences in bed file
Autobiographer
17 months 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: 1049 users visited in the last hour