User: p4alindromic

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p4alindromic10
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Posts by p4alindromic

<prev • 7 results • page 1 of 1 • next >
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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 15 days ago by p4alindromic10
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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 5 weeks ago by p4alindromic10
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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 5 weeks ago by p4alindromic10
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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 5 weeks ago by p4alindromic10 • updated 5 weeks ago by Mensur Dlakic2.2k
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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 3 months ago by p4alindromic10
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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 3 months ago by p4alindromic10 • updated 3 months ago by ATpoint26k
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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 3 months ago by p4alindromic10

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