User: rrbutleriii

gravatar for rrbutleriii
rrbutleriii60
Reputation:
60
Status:
Trusted
Location:
US, Chicago
Twitter:
@rrbiiiphd
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
1 year, 1 month ago
Email:
r**********@gmail.com

Posts by rrbutleriii

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
126
views
1
answers
Comment: C: Multiple rsIDs at chromosomal location?
... Follow up: So when parsing a vcf, would I then have to anticipate some variant callers giving me: `1 10051 rs1052373574;rs1326880612 A G,AC` I haven't ever seen that before, but I don't see anything to prohibit it. ...
written 6 weeks ago by rrbutleriii60
5
votes
1
answer
126
views
1
answer
Multiple rsIDs at chromosomal location?
... In the [VCF format][1], there is the option for the ID field to have multiple semi-colon separated values. In theory, there could be two dbSNP rsIDs in a single line (i.e. two indels at chr:pos), but for programming purposes, that should not happen, correct? dbSNP has merged all variants for a given ...
vcf annotation snp written 6 weeks ago by rrbutleriii60 • updated 6 weeks ago by Pierre Lindenbaum121k
0
votes
0
answers
143
views
0
answers
Applying lfcShrink to a time series analysis
... I am doing a time series analysis on a single cell line as in [Section 9][1] of the RNA-Seq workflow guide and was wondering if it is possible or advisable to apply lfc shrinkage to the result. library("fission") data("fission") ddsTC <- DESeqDataSet(fission, ~ strain + minute + stra ...
time-series deseq2 rna-seq written 10 weeks ago by rrbutleriii60
1
vote
1
answer
212
views
1
answers
Answer: A: From coverageBed to a list of reads per genes
... The reason the bam file is not working is because the bed file doesn't contain enough information to re-create reads. Perhaps there is a tool that attempts to reconstruct reads based on coverage beds, but that sounds...not good. You need a true bam/sam for featureCounts. I am unfamiliar with the ac ...
written 4 months ago by rrbutleriii60
0
votes
1
answer
235
views
1
answers
Answer: A: Questions about gene length and GC content in CQN normaliztion
... See this [post](https://www.biostars.org/p/317962/) for question one and two. Specifically, if all you need is gene length and GC, and you don't want to learn to access biomaRt directly, this will work (but takes a little time depending on the size of you matrix). library (EDASeq) ensembl_ ...
written 4 months ago by rrbutleriii60
1
vote
1
answer
408
views
1
answers
Comment: C: comparing RNA seq data from different studies using ratios
... The literal answer to 'would the ratio differ' is quite possibly. Thus my above that quantile normalized data shouldn't be compared in this way. Quantile normalization is not the same as the other normalization concepts of TPM/FPKM/RPKM. And even for those it is not recommended to compare across t ...
written 5 months ago by rrbutleriii60
0
votes
0
answers
206
views
0
answers
Pre-filtering transcriptome data by gene type
... I have seen in some transcriptome comparison analyses that the total RNA-seq data set is pre-filtered to only include protein-coding genes, or to exclude pseudogenes, or "short RNAs" ([Schwartzentruber et al](https://www.nature.com/articles/s41588-017-0005-8)). In a sense I understand this to imply ...
rna-seq non-coding rna transcriptome written 5 months ago by rrbutleriii60
2
votes
3
answers
615
views
3
answers
Answer: A: PacBio sequencing for variant calling?
... tl;dr The question to ask is the type of variation you are expecting to encounter; a non-systematic approach to be sure, but there is not a one size fits all solution. In my personal experience (TruSeq/Nextera Illumina several paired end types de novo and reference based, PacBio RSII p4c2/p5c3/p6c4 ...
written 5 months ago by rrbutleriii60
0
votes
1
answer
408
views
1
answers
Answer: A: comparing RNA seq data from different studies using ratios
... Read more in https://www.biostars.org/p/314454/ "The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the total protein-coding read count is replaced by the 75th percentile read count value for the sample." https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mR ...
written 5 months ago by rrbutleriii60
0
votes
0
answers
357
views
0
answers
Comment: C: Windows batch cmd for fastq-dump
... Indeed I have. This gets deep into the weeds of our institutional politics (of the type that would make Kafka blush). The short of it is this the actual server is airgapped, and virtual machine with internet access for the purposes of shuttling data is this one (a Win Server 2008 R2 OS, with heavily ...
written 6 months ago by rrbutleriii60

Latest awards to rrbutleriii

Supporter 4 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2124 users visited in the last hour