User: Ann

gravatar for Ann
Ann2.2k
Reputation:
2,240
Status:
Trusted
Location:
Concord NC USA
Website:
http://www.lorainelab....
Twitter:
aloraine205
Scholar ID:
Google Scholar Page
Last seen:
1 year, 2 months ago
Joined:
8 years, 4 months ago
Email:
a*******@gmail.com

Posts by Ann

<prev • 139 results • page 2 of 14 • next >
0
votes
2
answers
1.1k
views
2
answers
Comment: C: strange coordinates for Augustus-predicted gene
... Sorry, I just realized Augustus GFF does not report exons - just CDSs. ...
written 3.6 years ago by Ann2.2k
0
votes
2
answers
1.1k
views
2
answers
Comment: C: strange coordinates for Augustus-predicted gene
... I have a quick followup question about minus strand genes: Here is a line of data: scaffold3201|size9483 AUGUSTUS transcript 9115 0 0.86 - . ID=g68389.t1;Parent=g68389 According to this, the feature begins at base 9115 and ends at base 0. However, GFF is one-based. The st ...
written 3.6 years ago by Ann2.2k
0
votes
2
answers
1.1k
views
2
answers
Answer: A: strange coordinates for Augustus-predicted gene
... OK I will do that. I have written to person who made the file and he should be getting back to me very soon.     ...
written 3.6 years ago by Ann2.2k
5
votes
2
answers
1.1k
views
2
answers
strange coordinates for Augustus-predicted gene
... I'm writing a parser for Augustus GFF and have run into a weird case. Has anyone else seen this? At least one gene is listed with start greater than end, but only for the gene and transcript features. Everything else belonging to the gene has start less than end. # start gene g34050 scaffold424|s ...
augustus genefinder written 3.6 years ago by Ann2.2k
2
votes
4
answers
1.1k
views
4
answers
Answer: A: Upgrade to IGB 8.5.0 has lost my bookmarks and Quickload servers
... Hello Chris, I will notify the team and figure out what has happened. I'm very sorry for the inconvenience.  Losing bookmarks is not good. Yours, Ann ...
written 3.6 years ago by Ann2.2k
6
votes
0
answers
3.7k
views
0
answers
best alignment tool for Ion Torrent data
... Hello, I am teaching a Genomics Biotechnology class this semester at UNC Charlotte and have a question about the best alignment tool to use for a class project. Students in the class are using Ion Torrent PGM to sequence the chloroplast genomes of several different cultivars of tomato. The student ...
genome chloroplast iontorrent written 3.6 years ago by Ann2.2k • updated 3.5 years ago by Biostar ♦♦ 20
0
votes
2
answers
1.1k
views
2
answers
Answer: A: Inconsistent display of GFF files in IGB
... Great news on the paper! Bad news on the problem you have having with IGB. This sounds suspiciously like a known bug with a related format - GTF. See https://jira.transvar.org/browse/IGBF-809 Does this sound similar to what you're experiencing? A couple questions: Is the file on your Quickload ...
written 3.7 years ago by Ann2.2k
12
votes
0
answers
1.3k
views
0
answers
Forum: Please help support IGB software - need more letters of support
... Hello Biostars, The Integrated Genome Browser team would like to thank the community for using IGB and giving us great feedback over the years on how to make it better. A few weeks ago, we asked for your help. Our funding ends in July 2016, and we asked for letters of support from the community d ...
chip-seq forum visualization igb rna-seq written 3.7 years ago by Ann2.2k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Can't load BED file in IGB
... Hello - this is Ann, project lead for the IGB project. Thank you for your post - I hope you were able to move forward with your analysis. Also, if you think it would be a good idea for IGB to support loading data from multi-track files, please feel free to suggest it as new feature here: http://bi ...
written 3.7 years ago by Ann2.2k
1
vote
5
answers
2.5k
views
5
answers
Comment: C: Viewing the tophat output (mapped.bam and junctions) along with genome coordinat
... The new files are now available on IGBQuickLoad. IGB is now using the longer, non-numeric names for gene models. ...
written 4.0 years ago by Ann2.2k

Latest awards to Ann

Popular Question 23 months ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 23 months ago, created a question with more than 1,000 views. For looking for plant ChIP-Seq data sets to try DiffBind (need replicates)
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: visualize tiling array file to IGB
Popular Question 23 months ago, created a question with more than 1,000 views. For tophat2 reported the same alignment twice for the same read (paired end data)
Popular Question 23 months ago, created a question with more than 1,000 views. For need to separate read1 and read2 to run tophat2
Popular Question 23 months ago, created a question with more than 1,000 views. For Please help support IGB software - need more letters of support
Popular Question 23 months ago, created a question with more than 1,000 views. For Integrated Genome Browser version 8.3 released - new native installer
Popular Question 23 months ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.2 years ago, created a question with more than 1,000 views. For need to separate read1 and read2 to run tophat2
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Integrated Genome Browser version 8.3 released - new native installer
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 3.2 years ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 3.3 years ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: how to use a bed file with htseq-count
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Symposium And Rna-Seq Data Analysis Workshop Charlotte May 13-14
Popular Question 3.5 years ago, created a question with more than 1,000 views. For R packages for gene regulatory networks from time series data
Student 3.5 years ago, asked a question with at least 3 up-votes. For how to use a bed file with htseq-count

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 926 users visited in the last hour