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6.4 years ago
KVC_bioinfo
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Hello all,
I have downloaded the reference for the alignment from the following link:
How can I download gene list for this reference in order to visualize the alignment in IGV?
Thank you in advance.
This might sound naive, but is GRCh 37 and hg 19 same?
Take a look at this http://plindenbaum.blogspot.fr/2013/07/g1kv37-vs-hg19.html Some bases are different and there are different contig names. GRCh37 uses "chr1", "chr2", "chr3", and hg19 uses just the number.
Thank you. I was trying to download the gene list because I could not find a gene according to the coordinate in GRCh37/hg19 genome which is included in IGV. I have downloaded the reference I used from above link.
Once you load the genome, start typing in name of the gene of choice in search box. IGV will look the name up and present options. Select gene you need/want. IGV will automatically navigate to that region.
Primary sequence for GRCh37 and hg19 should be identical. Pierre's blog post is from 2013 and the differences mentioned there have likely been reconciled by now.
For all new analysis you should be using GRCh38. Any particular reason you are still using GRCh37? Leave the haplotypes/alternate sequences out unless you have a specific interest in them.
IGV is smart. It will use
chr1or1designations in your alignments for chromosomes. So it does not matter if you aligned using UCSC/Ensembl/NCBI nomenclatures.Thank you very much. searching the gene solved my problem. :)