4
votes
What are the conditions to perform Gene Expression Analysis on data you've performed RNA Sequence Analysis on?
The table pictured here is the result of a differential gene expression (DGE) test. In the table, each row is a gene (labeled with the gene ID and name) and each column (besides the first two) are the ...
2
votes
Calling isoforms from long read data generated from partially degraded RNA
I haven't used these long-read RNA-seq tools so I could be wrong here. Transcript reconstruction combines reads from the same transcript and should be robust to partial transcripts. In addition, ...
- 6,052
1
vote
How to make unrooted tree for Likelihood mapping result by using IQ2-tree?
You have provided two different trees. The second was the Arthropoda and labeled "image 2".
The first example the explanation is that it is an exact polytomy. I know this because the values ...
M__♦
- 8,428
1
vote
Calling isoforms from long read data generated from partially degraded RNA
You could have a go using LAST. I've been developing and using a protocol for mapping cDNA reads that is based around LAST-mapping since 2017. The most recent RY model addition in LAST seems to clean ...
- 12.4k
1
vote
Ubiquitous regulation of highly specific marker genes
You should make violin plots of the genes of interest (x-axis is your different clusters (i.e. cell-types) and y-axis is expression). Maybe they are differentially expressed but at the same time not ...
- 1,568
1
vote
Ubiquitous regulation of highly specific marker genes
An explanation in 3 parts
EDIT: The note above about looking at the violin plots may be useful, but again what your downstream analysis or experiment should impact your decision making.
TLDR: The ...
- 319
1
vote
hisat2 --rna-strandness option and downstream htseq-count analysis
Sample 2 looks comparable but Sample 1 shows a drastic reduction in unique alignments.
Your strandedness param is going to dictate how your alignments are done in the sense that discordant pairs will ...
- 1,568
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