User: matthew.m.hernandez

Reputation:
30
Status:
New User
Location:
Last seen:
1 year, 5 months ago
Joined:
3 years, 7 months ago
Email:
m******************@gmail.com

Posts by matthew.m.hernandez

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answer
538
views
1
answers
Comment: C: Differential Expression from Quantile-Norm Data
... Thanks for the advice Matina. Maybe you could provide further input, though. From the little that I've seen, the tutorials for those pipelines are based on individual samples +/- some condition and comparing gene expression. However, in this case, if my samples are cells from let's say 6 distinct pe ...
written 18 months ago by matthew.m.hernandez30
0
votes
1
answer
538
views
1
answers
Comment: C: Differential Expression from Quantile-Norm Data
... That's exactly what we're trying to do (both for comparing differentially expressed genes and for GSEA). ...
written 18 months ago by matthew.m.hernandez30
1
vote
0
answers
1.8k
views
0
answers
Comment: C: Fasta alignment to Tajima's D and population statistics
... Sorry for the late response Anand. I did not figure out what was going on with the BioPerl analysis. I ended up just sticking to DNAsp :-/ ...
written 18 months ago by matthew.m.hernandez30
0
votes
1
answer
538
views
1
answer
Differential Expression from Quantile-Norm Data
... Hi everyone, I'm a newbie to analyzing RNAseq data and wanted to get input on how to proceed forward with data that I received from my PI. The goal of the experiment was to compare gene expression across blood cells from different donors all under the same condition. There are donors of a given phe ...
differential-expression rna-seq written 18 months ago by matthew.m.hernandez30 • updated 18 months ago by Hussain Ather940
0
votes
0
answers
854
views
0
answers
Outgroup in DNA Alignment File (Nexus) (Network 5.0)
... Hi everyone, I'm essentially trying to avoid having to pay for additional software to work with the Network 5 phylogenetic [software][1] by converting my fasta alignment files to nexus files to create phylogenetic networks. I know how to do this, but what I would like to also do is to create an ou ...
root network dna alignment nexus outgroup written 2.7 years ago by matthew.m.hernandez30
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Fasta alignment to Tajima's D and population statistics
... Ahh, gotcha. Thanks for the insight! ...
written 3.2 years ago by matthew.m.hernandez30
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Fasta alignment to Tajima's D and population statistics
... Thanks for addressing the number of sequences flag! However, I'm still concerned with the theta value. Do you still have confidence in a difference between 0.00871 and 0.00958? ...
written 3.2 years ago by matthew.m.hernandez30
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Fasta alignment to Tajima's D and population statistics
... So this makes sense for the Pi value! However, this doesn't work for the theta statistic (2.16841/249 = 0.00871 which is pretty off from 0.00958). Of note, my sequence length is 249bp. ...
written 3.2 years ago by matthew.m.hernandez30
6
votes
0
answers
1.8k
views
0
answers
Fasta alignment to Tajima's D and population statistics
... Hi there, I'm a newbie who's trying to make use of the Bio::PopGen packages to analyze measurements of diversity in different populations of viral quasispecies. I can turn to DNAsp on Windows to analyze different FASTA alignments. This is straightforward and easy but takes a long time for 100 diffe ...
tajima popgen alignment bioperl statistics written 3.2 years ago by matthew.m.hernandez30
0
votes
0
answers
1.1k
views
0
answers
Highlighter Plot in R
... Hi everyone, I am trying to figure out if there is any available R method (or other alignment software) to create a clean visualization of a nucleotide alignment such as the one attached. Specifically, I have an alignment of nucleotide sequences in fasta file format and would like to portray the al ...
highlighter plot mismatches alignment R written 3.5 years ago by matthew.m.hernandez30

Latest awards to matthew.m.hernandez

Popular Question 18 months ago, created a question with more than 1,000 views. For Fasta alignment to Tajima's D and population statistics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2246 users visited in the last hour