Questions tagged [interval]
Questions related to processing, analysis, arithmetic, and set operations involving sequence intervals.
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questions
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`bedtools`: Intersecting/map into only one interval when there are multiple matches?
I have the following list of intervals
Chr
start
end
chr1
0
5
chr1
5
10
chr1
10
15
chr1
15
20
chr1
20
25
chr1
25
30
and the following CpGs I'd like to intersect with the intervals and ...
- 11
0
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Compare in Python / PyRanges two genomic intervals to determine whether they're separate, partially overlapping, or contained
As part of a larger analysis, I need to evaluate pairs of genomic regions (regionsA and regionsB) and perform different ...
- 131
2
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0
answers
32
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What Cellbase resources are 0-indexed, and which are 1-indexed?
The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
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4
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2k
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How to do `bedtools intersection` using pandas alone?
I have two pandas Dataframes, using python3.x:
...
- 1,393
1
vote
1
answer
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How to output only the overlapping region of two files?
I have two files of genomic coordinates. I am trying to output only the overlapping region of fileA if it intersects with fileB. Not the original fileA coordinates.
fileA
...
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4
votes
1
answer
195
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Find intervals that genes fall within their range
I am trying to run some frequency based stats to identify selective sweep in my study system using Rpackage "PopGenome".
To proceed with it I have split my genome data (whole genome sequencing) into ...
- 516
6
votes
3
answers
763
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Identify non-coding regions from a genome annotation
I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome:
...
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6
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3
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430
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Fast filtering of intervals not falling within a certain distance from known genes
I would like to filter a bed file with intervals, ie. in the format of:
chr1 13800 14301
chr1 15500 16001
chr1 19400 19901
chr1 22800 23301
...
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6
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2
answers
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Transcript Coordinate Ranges to Genomic Coordinates
I have 2 GFF3 files:
Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space.
Features using chromosome IDs as the landmarks. i.e. "exon" ...
6
votes
4
answers
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Any fast options to query large VCF bed intervals?
I'm doing some analysis and I need to subset a large VCF file (~8GB gziped) given a bed interval and identify within a subset of rsid.
Unfortunately, both my normal choices to do this analysis (<...
