User: gable_works

gravatar for gable_works
gable_works40
Reputation:
40
Status:
New User
Location:
Chicago
Last seen:
1 day, 20 hours ago
Joined:
1 year, 11 months ago
Email:
t*************@gmail.com

Posts by gable_works

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answer
464
views
1
answers
Comment: C: How to visualize narrowPeak file after peak calling using MACS?
... Sure. Are peaks not called from normalized read pileups? When looking at both a bedGraph and narrowPeak file this is much more detailed. The details in a bedGraph output for "visualization" can be just as informative as peaks and boundaries. MACS2 also outputs a summit file as to indicate the peak a ...
written 4 months ago by gable_works40
0
votes
1
answer
464
views
1
answers
Comment: C: How to visualize narrowPeak file after peak calling using MACS?
... Use `-B` during MACS2 call to create a bedGraph. ...
written 4 months ago by gable_works40
0
votes
0
answers
409
views
0
answers
Comment: C: ATAC-seq data and deepTools: Small detail with impact on output
... I see now that in the later text this is stated. But this still begs the question as to why the outputs are different. If you say that nearly all of my library will be analyzed as paired end fragments then why does `-e` make a difference? And do you have any alternatives to analyze cut sites? If you ...
written 4 months ago by gable_works40
0
votes
0
answers
409
views
0
answers
Comment: C: ATAC-seq data and deepTools: Small detail with impact on output
... I would recommend that if you are only interested in cut sites from ATAC data, excluding the `-e` option is an incomplete solution. I'm assuming that the interpretation of a cut site is actually the end of the fragments that are aligned in the paired end file. I can reason that to what degree (how m ...
written 4 months ago by gable_works40
0
votes
0
answers
409
views
0
answers
Comment: C: ATAC-seq data and deepTools: Small detail with impact on output
... Thank you for bringing this up. Certainly Tn5 occupies space on the genome which we want to somehow incorporate into our analysis. But how much space? My reference highlights a 25/30 mer sequence insertional bias for the Tn5 on the bacterial genome [Mobile DNA][1]. The original publication that came ...
written 4 months ago by gable_works40
0
votes
0
answers
409
views
0
answers
Comment: C: ATAC-seq data and deepTools: Small detail with impact on output
... Also I should have directed my > to < I have updated the post*** ...
written 4 months ago by gable_works40
1
vote
0
answers
409
views
0
answers
Comment: C: ATAC-seq data and deepTools: Small detail with impact on output
... Please confirm that images are posted correctly. ...
written 4 months ago by gable_works40
0
votes
0
answers
409
views
0
answers
Comment: C: ATAC-seq data and deepTools: Small detail with impact on output
... I do understand that `-e` is recommended. "*Paired-end:* Reads with mates are always extended to match the fragment size defined by the two read mates. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. ...
written 4 months ago by gable_works40
10
votes
0
answers
409
views
0
answers
ATAC-seq data and deepTools: Small detail with impact on output
... I use deepTools regularly in my pipelines. For ATAC-seq data I noticed a potential downside to the `bamCoverage` function. My sequence read length is 2x42 and alignment paired end. With the assumption that deepTools bamCoverage would align read fragments according to mated pairs, I found a small det ...
atacseq deeptools readlength bigwig forum written 4 months ago by gable_works40 • updated 4 months ago by ATpoint36k
0
votes
1
answer
710
views
1
answers
Comment: C: Motif analysis from H3K27ac ChIPseq broad peaks
... The motifs bound by TFs are most likely within the valleys of your H3K27ac signal. This hypothesis has been tested [(article)][1] and a program called [EpiSAFARI][2] was developed to identify peaks within valleys . You can certainly do motif analysis on the peak set you have but it wouldn't make mus ...
written 4 months ago by gable_works40

Latest awards to gable_works

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 769 users visited in the last hour