Question: new regions in GRCh38
1
gravatar for skanterakis
4.0 years ago by
skanterakis110
United Kingdom
skanterakis110 wrote:

Hello, I wanted to inspect the (non-N) regions that were added in, in GRCh38/hg38 that were not there in GRCh37/hg19. Is there a hg38 bed file with those "new" regions somewhere or is there an easy way to get that without lifting over again? Thanks for your help!

hg19 human reference grch38 grch37 • 1.2k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by skanterakis110

See these posts:

A: How to determine reference genome that was used for alignment given BAM with obs

A: Convert BED(UCSC) to VCF

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by natasha.sernova3.7k
3
gravatar for skanterakis
4.0 years ago by
skanterakis110
United Kingdom
skanterakis110 wrote:

I used the excellent remap service from NCBI: http://www.ncbi.nlm.nih.gov/genome/tools/remap

to go from my hg19 assembly to my hg38 assembly.

I made a dummy bed file using the chromosome lengths, which you can get from here:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo" > hg19.genome

and selected:

Minimum ratio of bases that must be remapped: 0

Maximum ratio for difference between source length and target length: 100000

and that gave me all possible mappings.

ADD COMMENTlink written 4.0 years ago by skanterakis110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 977 users visited in the last hour