8
votes
Accepted
Working with old genome builds
In my opinion, it is not very reliable. LiftOver is very limited in terms of transformations it can support. The LiftOver Chain format can capture only matching regions in the same order. It means ...
- 1,899
4
votes
Ensembl protein identifiers from different assemblies
Those IDs are elderly! Ensembl 54 was 2009!
I would recommend using BioMart combined with the ID history converter. The ID history converter will convert old IDs to new, and BioMart will convert ...
- 1,749
4
votes
Working with old genome builds
I think that right now, the only human builds that are worth considering are hg19/GRCh37 as many data bases such as gnomAD still exclusively use this release. On the other hand, hg38/GRCh8 has many ...
- 588
3
votes
Accepted
What is the `table` parameter in the UCSU ldHgGene tool?
I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of ...
- 46
3
votes
How can I compare two bed files?
From a set operations viewpoint, consider your hg37 regions as a "reference" set and hg38 as a "map" set.
If you have these sets in BED format, BEDOPS lets you do set operations on them with various ...
- 3,125
2
votes
How can I compare two bed files?
I wrote ParsEval to handle these types of comparisons. ParsEval reports a variety of similarity statistics at both the nucleotide level and feature (exon) level. It doesn't explicitly support "fuzzy" ...
- 5,060
2
votes
Working with old genome builds
You could use liftOver which isn't always great.
Whenever I encounter this (especially NGS data readily available on the SRA), I often just get the raw files (e.g. fastqs) and re-align/re-map.
In ...
- 1,563
2
votes
Accepted
Accessing UCSC genome via ssh results in a validation error
You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys:
http://genomewiki.ucsc.edu/index.php/...
- 81
2
votes
How do I lift GWAS results to hg38?
Yes. LiftOver tools, if they work on VCF data (some only take BED as input) work on GWAS summary statistics. You could use
https://pypi.org/project/liftover/, for example.
- 364
2
votes
Accepted
Lifting from hg38 to hg37
BED format can refer to the ".txt" file format that stores chromosomes and positions of genomic features as well as some other things like name. bed ...
- 857
2
votes
How important are the homozygous variants that get unnecessarily deleted using liftover?
All this is saying is that the tool doesn't lift over variants which aren't present in the vcf. I can't imagine this being a big deal in any analysis I've done and it's exactly what I'd expect the ...
- 1,621
1
vote
Lifting snp rsid build 37 to 38
There are multiple tools to use for this. Might I suggest the following reads: Introduction to liftover tools, where they also refer to this usefull post BioStars post. Maybe also consider reading ...
- 159
1
vote
Accepted
Large amount of REF prefix differences after lifting
It is important that after lifting over a VCF/BCF file from one coordinate system to another, the header of the resulting file contains the chromosome/contig names as present in the coordinate system ...
- 750
1
vote
How do I lift GWAS results to hg38?
I would advise against using dbSNP rsIDs to perform a liftover as they get updated over time. I recently wrote a software to liftover summary statistics and the documentation includes instructions ...
- 117
1
vote
How do I lift GWAS results to hg38?
It turned out to be easier than expected. You figure out which dbSNP version they used. dbSNP is the classification system for snps based on the rsid format. Pretty much every GWAS publishes their ...
- 181
1
vote
Accepted
UCSC liftover cannot produce bed format output
I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":"
I removed ":" and it worked
- 282
1
vote
hgsql not found when running a script despite being accessible on command-line
It is possible that the shell being used in the process is different from your standard command line shell. I am not familiar with the tool, and it's hard to say more without knowing your OSX version, ...
- 3,649
1
vote
dog coordinates (canFam3) to human coordinates (hg19)
Based on this old answer, this is not recommended for liftOver. For between-species liftovers, it is claimed that you are likely to want a different tool such as pslMap. For a lot of rather detailed ...
- 3,649
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