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Search: Posts Made By: Joseph White
Forum: Bioinformatics 12-13-2019, 10:16 AM
Replies: 0
Views: 803
Posted By Joseph White
Coding exon vs All exons

Hi Everyone,

The UCSC genome browser allows us to download all exonic regions. There are several options which affect the output, including:

"Exons plus "
"Coding exons"
etc

The exons+...
Forum: Bioinformatics 12-13-2019, 09:47 AM
Replies: 0
Views: 771
Posted By Joseph White
Non-standard amino acid code in CADD

Hi Everyone,

The CADD data set from Washington U., lists annotation for all potential variants in the human genome, including annotation about amino acid changes. The single letter amino acid...
Forum: Bioinformatics 12-10-2018, 12:14 PM
Replies: 0
Views: 600
Posted By Joseph White
Has anyone here used ALoFT with GRCh38 ?

Hi Everyone,

We are looking at 'loss of function' variants in the human genome. I am using a program called 'ALoFT' to identify LoF variants. Problem is that my data has GRCh38 chromosome and...
Forum: Bioinformatics 05-09-2018, 06:11 AM
Replies: 7
Views: 2,131
Posted By Joseph White
Oh, that's right. All I have to do is add a...

Oh, that's right. All I have to do is add a third column of '.' to make it VCF. Thanks.
Forum: Bioinformatics 05-09-2018, 05:50 AM
Replies: 7
Views: 2,131
Posted By Joseph White
The file is not in BED, GFF, or SAM format.

The file is not in BED, GFF, or SAM format.
Forum: Bioinformatics 05-09-2018, 03:04 AM
Replies: 7
Views: 2,131
Posted By Joseph White
best way to index tab-delimited text file

What is the best way to index a tab-delimited text file containing chromosome, position and variant data? My files are huge and too big to maintain in memory, so indexing seems the only viable...
Forum: Bioinformatics 05-01-2017, 10:53 AM
Replies: 1
Views: 1,190
Posted By Joseph White
Baits in WGS???

Hi,

Capture baits are used for exome sequencing in WES. Are baits used for whole genome sequencing. Or, is sequencing randomly primed for WGS?

Thanks for any info.
Cheers,
jwhite
Forum: Bioinformatics 01-12-2017, 10:07 AM
Replies: 0
Views: 1,473
Posted By Joseph White
pR2 function fails on fully populated R object

Hi,

The R package, pscl, is meant for statistical analysis. The pR2 function that calculates "pseudo R-sq" has been failing with error:

"no applicable method for 'pR2' applied to an object of...
Showing results 1 to 8 of 8

 


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