User: p4alindromic

gravatar for p4alindromic
p4alindromic10
Reputation:
10
Status:
New User
Location:
Last seen:
8 months, 3 weeks ago
Joined:
11 months, 3 weeks ago
Email:
p***********@yandex.com

Posts by p4alindromic

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
2.3k
views
1
answers
Comment: C: MACS2 option for ATAC seq?
... I think so. When I use `--nomodel -- shift -100 -- extsize 200 -f BED` I have 1.5 times more peaks compared to `--nomodel -- shift -100 -- extsize 200 -f BAM`. ...
written 9 months ago by p4alindromic10
0
votes
1
answer
267
views
1
answers
Comment: C: Scaffolds and contigs in the assembled genomes
... I read that but what does "not yet mapped" mean? That still leaves my questions unanswered: Are they actually part of the chromosomes (do we have gaps in the current chromosome assembly that these sequences could be later mapped confidently)? Can parts of these sequences be the same as the ones in ...
written 9 months ago by p4alindromic10
0
votes
1
answer
267
views
1
answers
Comment: C: Scaffolds and contigs in the assembled genomes
... Thanks for the reply. My second question is actually about the fasta entries in the "nonchromosomal" file in the following link: ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/ I am assuming these are scaffolds/contigs that are not part of the assembled chromosomes. Is that correct? If ...
written 9 months ago by p4alindromic10
1
vote
1
answer
267
views
1
answer
Scaffolds and contigs in the assembled genomes
... I have several questions regarding the scaffolds and contigs. Are they pieces of DNA that are assembled into contigs and scaffolds but cannot be confidently combined with chromosome assembly? Do they already have corresponding sequences in the assembled chromosomes, or is their sequence compositio ...
alignment scaffold written 9 months ago by p4alindromic10 • updated 9 months ago by Mensur Dlakic6.0k
0
votes
1
answer
602
views
1
answers
Comment: C: How is distal enhancer defined?
... I think in the second paper, proximal means promoter and distal means enhancer. I am more interested in classifying an enhancer based on it being relatively close to a gene or quite distant from a gene. What would be an approximate distance threshold then? ...
written 11 months ago by p4alindromic10
3
votes
1
answer
602
views
1
answer
How is distal enhancer defined?
... How distant to a gene does an enhancer have to be to be called as distal enhancer? Is there an agreed upon distance for this? Quick search on the web did not give me a clear answer. Thanks! ...
enhancer written 11 months ago by p4alindromic10 • updated 11 months ago by ATpoint36k
0
votes
0
answers
294
views
0
answers
Differentially accessible and known enhancer overlap
... Hi everyone, I want to see if my differentially accessible peaks that I obtained from ATAC-seq comparisons overlap with known enhancers. I read people using bedtools intersect to see if there is overlap but there is usually no mention of the minimum length/percentage of overlap required. What would ...
bedtools enhancer atac-seq written 11 months ago by p4alindromic10

Latest awards to p4alindromic

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: 673 users visited in the last hour