8

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 that it can account for indels, but even simple structural variations become problematic. For instance, when a newer assembly is available, it is usually a ...


4

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 important fixes and the useful (but yet underused) feature of alternative loci. Anything from older releases should be remapped to a more recent one.


4

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 ENSPs to ENSGs. You can either use the ID history converter with the ENSPs first, then the current BioMart to get the ENSGs. Or you can use Ensembl 54 BioMart to ...


3

I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of lgHgGene, the database parameter is ignored but must still be provided. The table parameter should be the second column from your GTF file. Note that you must also specify the -gtf option (otherwise it expects GFF format). In my case, the GTF file ...


3

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 overlap criteria. Specifically, you can use BEDOPS bedmap to map hg38 regions to hg37 regions. The bedmap tool lets you assign overlap criteria from as little ...


2

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 format can also refer to the plink format, which belongs to bed, bim, fam trio. The plink bed format stores all the genetic variants, but the program needs to refer to bim file for their positions. ...


2

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/Parasol_job_control_system#SSH_keysssh key setup


2

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" matches, but it does report scaled values between 0.0 and 1.0 for similarity, so you could get a similar feel by definig a similarity cutoff for filtering. ...


2

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 your case (arrays) it may be a bit tough. Not impossible though, as I recently took some old yeast DNA/RNA microarray data and updated it to the newest genome. ...


1

I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":" I removed ":" and it worked


1

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, but it looks like it is using zsh. I think that zsh only fairly recently became the standard OSX shell. I don't know the tool or the shell very well, but it ...


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