User: Jingyue
Jingyue • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United States
- Last seen:
- 2 days, 20 hours ago
- Joined:
- 5 years, 8 months ago
- Email:
- j***********@uconn.edu
Posts by Jingyue
<prev
• 32 results •
page 1 of 4 •
next >
0
votes
1
answer
955
views
1
answers
... I have been using narrowPeak files for downstream analysis (annotation, motif finding, differential peak calling), should I use the summits.bed or narrowPeak files?
I'm asking this because narrowPeak files have many peaks start-end ranges if use --call-summits in MACS2. So I only keep 1 unique peak ...
written 26 days ago by
Jingyue • 30
0
votes
1
answer
5.1k
views
1
answers
Comment:
C: DESeq2 compare all levels
... Thank you for the help! ...
written 5 weeks ago by
Jingyue • 30
0
votes
1
answer
5.1k
views
1
answers
Comment:
C: DESeq2 compare all levels
... Hello, Did you solve this? It happens to me as well! Thanks! ...
written 5 weeks ago by
Jingyue • 30
0
votes
3
answers
510
views
3
answers
... Download the bed file from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables).
Set the parameters as shown below:
- clade: Mammal
- genome: Human
- assembly: 2009(GRCh37/hg19)
- group: Genes and Gene Predictions
- track: select the one that fits your experimental pur ...
written 7 weeks ago by
Jingyue • 30
0
votes
0
answers
314
views
0
answers
... Dear Community,
We are starting a new lab in College of Agriculture and Life Sciences at Cornell. We will have 2 PhD research assistant positions in animal functional genomics and bioinformatics available at Cornell Animal Science in 2021 Fall (Postdoc positions are also available). Please find our ...
written 3 months ago by
Jingyue • 30
0
votes
3
answers
6.2k
views
3
answers
Comment:
C: ATAC-seq DE analysis
... Thanks for your answer!
I'm wondering do you use DEseq2 or EdgeR for differential analysis on these merged read counts coverage files? I thought they all need sample replicates as input.
Thank you!
...
written 11 months ago by
Jingyue • 30
2
votes
2
answers
1.0k
views
5 follow
2
answers
... Dear all,
I saw having the mapped reads have +4 and -5 shift in ATAC-seq is a common practice.
Some place says "reads should be shifted + 4 bp and − 5 bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase and ach ...
written 11 months ago by
Jingyue • 30
• updated
9 weeks ago by
Devon Ryan ♦ 98k
0
votes
3
answers
1.2k
views
3
answers
Comment:
C: ATAC-seq 150bp reads
... Hi, ATpoint,
Thanks for the insightful answer!
I plan to send out my sample for sequencing. Do you think sequencing ATAC library at a short length directly would be better? Like 35bp paired end reads. Or do long reads 150bp and then clip it shorter by some tools?
Thank you! ...
written 13 months ago by
Jingyue • 30
0
votes
5
answers
6.9k
views
5
answers
... Hello,
Do you also merge the differential binding regions among these different tools?
Thanks! ...
written 17 months ago by
Jingyue • 30
0
votes
0
answers
343
views
0
answers
... Hello all,
Do you recommend to overlap two or more differential peak calling tools to get a more stringent/accurate differential peaks?
Thank you! ...
written 17 months ago by
Jingyue • 30
Latest awards to Jingyue
Popular Question
10 days ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Supporter
19 months ago,
voted at least 25 times.
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
3.6 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
4.7 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1128 users visited in the last hour