Questions tagged [interval]

Questions related to processing, analysis, arithmetic, and set operations involving sequence intervals.

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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 ...
basesorbytes's user avatar
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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 ...
Einar's user avatar
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2 votes
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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 ...
mRotten's user avatar
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7 votes
4 answers

How to do `bedtools intersection` using pandas alone?

I have two pandas Dataframes, using python3.x: ...
EB2127's user avatar
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1 vote
1 answer

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 ...
Michael Lee's user avatar
4 votes
1 answer

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 ...
Anna1364's user avatar
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6 votes
3 answers

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: ...
Angel's user avatar
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6 votes
3 answers

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 ...
gc5's user avatar
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6 votes
2 answers

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" ...
Nathan S. Watson-Haigh's user avatar
6 votes
4 answers

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 (<...
andremrsantos's user avatar