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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 ...
  • 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 ...
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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