User: nancydong20

gravatar for nancydong20
nancydong2080
Reputation:
80
Status:
Trusted
Location:
Last seen:
12 months ago
Joined:
1 year, 8 months ago
Email:
n**********@gmail.com

Posts by nancydong20

<prev • 41 results • page 1 of 5 • next >
0
votes
0
answers
335
views
0
answers
Predicted complete ORFs that are identical to cDNA clones but have no BLAST hits
... Hello! I assembled a number of transcripts from a non-model organism and used TransDecoder to predict ones with complete ORFs. I see that a number of the transcripts containing complete ORFs don't have a hit in protein or RNA BLAST databases, but are identical to entries in the BLAST EST database f ...
rna-seq written 12 months ago by nancydong2080
0
votes
1
answer
452
views
1
answers
Comment: C: WGCNA analysis for normalised data expression data sets
... Well, trait data can be added in later if you find a particular module of interest and think that it could be correlated with a trait that you are seeing (just my random guess, like if you are seeing variations in how well each sample is "developing"). Integrating trait data basically allows you to ...
written 13 months ago by nancydong2080
1
vote
1
answer
2.9k
views
1
answers
Comment: C: HISAT2 software installation
... Yes, conda works with Linux. You can think of it as kinda like perlbrew for python. But it really doesn't seem like an installation issue if your original .`/hista2` command worked. You can download and install Miniconda on Linux from here: https://conda.io/miniconda.html After installing Minicon ...
written 13 months ago by nancydong2080
0
votes
1
answer
2.9k
views
1
answers
Answer: A: HISAT2 software installation
... First, this doesn't seem to be an installation issue. You can try installing hisat2 using conda, which will give a more hassle-free installation. Is the hisat2 folder in your PATH? If not, then just typing `hisat2 -h` would likely give you "command not found". I see in your first post that you used ...
written 13 months ago by nancydong2080
0
votes
0
answers
624
views
0
answers
Bayesian network analysis of RNA-seq data to infer upstream/downstream genes
... Hello! I am currently using RNA-seq to examine the roles of a few key proteins in the transcriptional response underlying a certain condition. I came across this interesting [article][1] where Bayesian Network Analysis (using the R package *deal*) was used to analyze RNA-seq data to infer which ge ...
bayesian network analysis rna-seq written 13 months ago by nancydong2080
0
votes
1
answer
571
views
1
answers
Comment: C: Examining connectivity of specific genes in WGCNA
... Fantastic, I will go look at that. Thank you very much! ...
written 13 months ago by nancydong2080
0
votes
1
answer
571
views
1
answers
Comment: C: Examining connectivity of specific genes in WGCNA
... Thank you very much for the suggestions! Regarding your suggestion #3, if I have three experimental groups such as control, "stimulated" and knockdown+"stimulated", do I need 35 samples per group? As a side question, is WGCNA a suitable approach if I this is what I'm planning: 1. First characte ...
written 13 months ago by nancydong2080
0
votes
1
answer
571
views
1
answers
Comment: C: Examining connectivity of specific genes in WGCNA
... Thank you very much! ...
written 13 months ago by nancydong2080
3
votes
1
answer
571
views
1
answer
Examining connectivity of specific genes in WGCNA
... Hello! I am currently learning about WGCNA as preparation for an up-coming project, studying a potential novel transcription factor. I am interested in seeing which genes are expressed in a correlated manner with my transcription factor, can WGCNA be used for this? Thank you very much for shedding ...
wgcna written 13 months ago by nancydong2080 • updated 13 months ago by ildem20
1
vote
0
answers
962
views
0
answers
RepeatModeler and RepeatMasker for non-model species
... Hello everyone! I am trying to analyze repeat elements in a new draft genome of a non-model organism. I used RepeatModeler to build a *de novo* repeat library, and then used RepeatMasker (rmblastn version 2.2.27+) to mask the genome. In the .tbl output, I see that no simple repeats or low complexi ...
repeatmasker repeatmodeler written 14 months ago by nancydong2080

Latest awards to nancydong20

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: 797 users visited in the last hour