User: xiaofeiwang198266
xiaofeiwang198266 • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- United States
- Last seen:
- 1 year, 7 months ago
- Joined:
- 4 years, 6 months ago
- Email:
- x****************@gmail.com
Posts by xiaofeiwang198266
<prev
• 20 results •
page 1 of 2 •
next >
0
votes
0
answers
832
views
0
answers
Comment:
C: HOMER target sequence location
... I have the same concern, did you figure it out.
I am trying to use "Finding Instance of Specific Motifs" http://homer.ucsd.edu/homer/ngs/peakMotifs.html, but the results do not like what I am expected. Because the number of peaks/targets is not same as the number "knownResults.txt". ...
written 19 months ago by
xiaofeiwang198266 • 20
0
votes
0
answers
734
views
0
answers
... Dear folks,
Does anyone have experience using getDifferentialPeaksReplicates.pl in HOMER, which is new added to HOMER in this Feb. It uses R/Bioconductor and DESeq2 (by default) to perform the differential enrichment calculations. But, I don't know why I got negative tag count for my results? I pa ...
written 20 months ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.1k
views
1
answers
Comment:
C: Motif finding with HOMER
... answer the problem just for people who got same problem:
Figure the problem out by installing weblogs and newer version of Ghostscript (9.10). ...
written 21 months ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.1k
views
1
answers
Comment:
C: Motif finding with HOMER
... Did you figure out your problems? I got same problem. (I used it many years ago, it worked well but now, I did not make it work. I see this "Sequence logos produced during motif finding are now rendered using SVG instead of relying on weblogo/ghostscript." http://homer.ucsd.edu/homer/. But, I did no ...
written 21 months ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.8k
views
1
answers
... H3K4me3 is associated with transcriptional activation. If there is enrichment for this histone mark, it is expected that the gene should be activated expressed. Am I right? ...
written 22 months ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.6k
views
1
answers
Comment:
C: Homer detailed annotation
... Also, I downloaded hg18 genome to see the difference with my custom genome. There are lots of information under ~/software/homer/data/genome/hg18:
chrom.sizes
hg18.rna
hg18.tts
hg18.tss
hg18.stop
hg18.splice5p
hg18.splice3p
hg18.miRNA
hg18.aug
hg18.repeats
hg18.basic.annotation
hg18.full.annotation ...
written 2.0 years ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.6k
views
1
answers
Comment:
C: Homer detailed annotation
... Sorghum bicolor. Does is matter for this? On my understanding, "loadGenome.pl" is to prepare a custom genome for use with HOMER, so I don't think it will pull any information from Homer? ...
written 2.0 years ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.6k
views
1
answers
Comment:
C: Homer detailed annotation
... I tired this
but got this
"Could not find full/detailed annotation file (~/software/homer/.//data/genomes/sorgBi1.31//sorgBi1.31.annotation)"
I think I need this detailed annotation filed created when use loadGenome.pl, but don't know how or why it is not generated when using loadGenome.pl. ...
written 2.0 years ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.6k
views
1
answers
Comment:
C: Homer detailed annotation
... I will try and let people know. ...
written 2.0 years ago by
xiaofeiwang198266 • 20
0
votes
1
answer
1.6k
views
1
answers
Comment:
C: Homer detailed annotation
... Could I ask another question? It is about pos2bed.pl not associated with this one. Or, do I need to open another thread?
...
written 2.0 years ago by
xiaofeiwang198266 • 20
Latest awards to xiaofeiwang198266
Popular Question
22 months ago,
created a question with more than 1,000 views.
For a question about -unitigs.fa and -scaffolds.fa
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1236 users visited in the last hour