Hi,
I want to look at raw sequencing reads. Ideally I would like to
check both base calls and sequence quality scores (including
information about number and quality of reads) for specific stretches
of sequence.
The reason for doing this is because on 28 way multi-genomic
alignments--some of the aligned sequences from other species have stop
codons within the coding exon, and I want to check how confident the
sequence quality is.
This is an example of my queries:
I wanted to look for orthologs for the human IGLC1 gene within other
species. I did this by searching on the human chromosomal location
for this gene- chr22: 21567554-21567874 (Human March 06 assembly). I
wanted only placental mammal orthologs, so I selected this option, and
then obtained the vertebrate multiz alignment and phastcons
conservation for 28 species. I then chose the options "Capitalize
coding exons based on Ensembl genes" from the pulldown menu on top of
the page.
Here is the link:
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=132217768&o=21567553&t=21567874&g=multiz28way&i=multiz28way&c=chr22&l=21567553&r=21567874&db=hg18&pix=800
I then take the capitalized nucleotide sequences for all the species
and translate them into protein. When I do this, with the Bushbaby
and Hamster sequences, I get several stop codons early on in the
protein. Are these stop codons real or could they be due to the
quality of the sequencing reads?
My OS is MacOSX and I am using a Safari browser.
I hope I have been clear and provided sufficient detail. I would
really appreciate any help and/or advice.
Thanks,
Dr. Meenakshi Roy
UCLA
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