User: mrz132435

gravatar for mrz132435
mrz13243520
Reputation:
20
Status:
New User
Location:
Last seen:
5 days, 18 hours ago
Joined:
2 years, 8 months ago
Email:
z********@osu.edu

Posts by mrz132435

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
84
views
1
answer
Comparing gene expression for individual gene between samples in R
... Hi. I have whole exome raw count data for a bunch of samples, and I'm looking to compare gene expression *for a single gene* between samples, e.g., between samples that have some type of mutation in said gene and samples that don't. I'd like to do this analysis over a set of genes, but each one indi ...
R rna-seq written 5 days ago by mrz13243520 • updated 5 days ago by swbarnes27.0k
0
votes
0
answers
138
views
0
answers
Is it possible to get reference allele info at each position within a range from a bam file in Rsamtools?
... How do I get info about which base matches to the reference genome from a bam file? Specifically, is it possible to do this in Rsamtools? Using the code below (where 'bam' and 'bai' have already been defined as the bam and bai file paths) I can use pileup get a data frame that has the counts for eac ...
R sequencing written 3 months ago by mrz13243520
4
votes
3
answers
253
views
6 follow
3
answers
Why does every database have a different set of exons for TP53 (and other genes)?
... I was looking to get the start and stop positions for all exons in TP53, and of course there are a few ways to do this in R. It is generally believed that [TP53 has 11 exons](https://omim.org/entry/191170). And yet, each method I use to pull exon info finds a different number. Using biomaRt, I got 5 ...
gene R ensemble exons written 4 months ago by mrz13243520 • updated 4 months ago by i.sudbery6.3k
0
votes
1
answer
162
views
1
answer
How to efficiently get reference bases (hg19) for a list of SNV loci (e.g., from a MAF file)?
... I have an MAF file with about a couple million SNVs in it from various samples, and I'd like to verify that the file has the right reference bases. Since I'm not really looking for a 'sequence' it seems like querying Ensembl for each one wouldn't be vey efficient. Is there any straightforward way to ...
maf snv written 4 months ago by mrz13243520 • updated 4 months ago by manuel.belmadani1.1k
0
votes
1
answer
800
views
1
answers
Comment: C: SNP Array data with 0 copies for a segment
... The data is from tumor samples. It's leukemia so the cancer cells are (I've been told) fairly easy to isolate, so normal contamination should be negligible. So it is somatic copy number alterations I'm interested in; there are clearly plenty there too, just not sure what to expect when both copies o ...
written 2.7 years ago by mrz13243520
1
vote
1
answer
800
views
1
answer
SNP Array data with 0 copies for a segment
... Hello, I am working with SNP array data and would like to know what I should expect to see when a genome has lost both alleles at a segment. The issue is, data for SNP arrays is reported as the Log2 R Ratio (LRR) and the B allele fraction (BAF). The LRR is supposed to be Log2(cn/2) where cn is th ...
copy number snp cgh written 2.7 years ago by mrz13243520 • updated 2.7 years ago by bernatgel2.2k

Latest awards to mrz132435

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 856 users visited in the last hour