Daily Archives: May 2, 2019

GM12878 Updated Phased Trancriptome

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Q:
I noticed that you have an updated version of the GM12878 diploid genome
on the AlleleSeq webpage, but not an updated version of the transcriptome.
Would you be willing to upload an update for the transcriptome as well?
Also, are there major differences between the versions?

I actually now see how to generate the transcriptome myself using
vcf2diploid and the vcf file mentioned in the README (which I hadn’t noticed
before). Do you believe this vcf
(ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.2/hg19/CEUTrio.HiSeq.WGS.b37.bestPractices.phased.hg19.vcf.gz)
is the most accurate?

I’m actually trying to use liftover with the chain files from the newest diploid genotypes you created to update an annotation. However, the annotation ends up being empty. Have you experienced a similar problem? I’m using the hg19 UCSC annotation. Any help you can provide would be MUCH appreciated!

A:
Your chain file does not include ‘chr’ in front of the reference names.

List of all PDB structures + chain IDs for motions database

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Q:

I would like to have information on the list of PDB structures (with chain IDs) for the structure pairs used in the motions database. I saw that the zipped list file of IDs in the website did not have the chain ID. I was wondering if you have already compiled information available for this?

I was a bit confused by the format of the file available for download on MolMovDb website (List.txt.gz). Do you have a compiled list of just the motion pairs manually created and for which PDB structures are available? I am also specifically looking for the corresponding chain ID for each of the PDB structures. Any help would be appreciated!

A:
Fairly recently, we virtualized MolMovDB, and this process
may have made it difficult to obtain some of the data files for which you’re
searching. This may also have played a role in the issue you bring up
about the
filters.