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Search: Posts Made By: cristae8
Forum: Bioinformatics 09-08-2011, 12:38 PM
Replies: 0
Views: 2,033
Posted By cristae8
Translating amino acid position to chromosomal location

Hi,
I was wondering if someone has developed a tool to translate amino acid position in a gene (ie, amino acid 100) to the corresponding chromosomal location, including strand info. Any...
Forum: Bioinformatics 08-05-2011, 09:04 AM
Replies: 3
Views: 4,321
Posted By cristae8
Samtools mpileup/bcftools

Hi all,
I read through samtools manuals several times, but I'm still not clear on how exactly samtools & bcftools decide to call a SNP. I've tried to run through multiple combination of arguments...
Forum: Bioinformatics 07-21-2011, 02:50 PM
Replies: 5
Views: 2,903
Posted By cristae8
Thanks, everyone. bedTools seems to work the best...

Thanks, everyone. bedTools seems to work the best and it's fully documented so very easy to use! Much thanks to Aaron (the author) & Pete.
Forum: Bioinformatics 07-19-2011, 02:22 PM
Replies: 5
Views: 2,903
Posted By cristae8
Question *** Per base coverage ***

Hi,
This seems like a silly question, but I can't quite find the answer for it anywhere. I have a list of single nucleotide position, ie,
chr 1 72342
chr 2 32912
chr X 184343
etc,
to which I...
Forum: Bioinformatics 06-17-2011, 04:22 PM
Replies: 6
Views: 11,892
Posted By cristae8
Thanks, DerSeb! Regarding my 2nd question,...

Thanks, DerSeb!

Regarding my 2nd question, I realized that error was because tabix (called inside fill-rsIDs) was not on my path.
Forum: Bioinformatics 06-16-2011, 01:22 PM
Replies: 6
Views: 11,892
Posted By cristae8
Unhappy Samtools mpileup on multiple samples

Hi,
I have multiple samples from which I would like to call SNP. I've been trying either to call them separately or all at once

samtools mpileup -uf hg19.fa sample1.bam | bcftools view -bvcg - >...
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