Tricks and tips for everyone


How do you compare transcriptome?

How do you compare transcriptome?

To compare transcriptomes between any two species, a first step is to establish homologous relationships between proteins in the two species. A second step is to identify expression data obtained from experiments that are performed under similar conditions or tissue types.

What is meant by transcriptome assembly?

De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome.

How many reads for transcriptome assembly?

Experiments looking to get an in-depth view of the transcriptome, or to assemble new transcripts, may require 100–200 million reads. In these cases, researchers may need to sequence multiple samples across several high output sequencing lanes.

How does transcriptome analysis work?

Transcriptome analysis experiments enable researchers to characterize transcriptional activity (coding and non-coding), focus on a subset of relevant target genes and transcripts, or profile thousands of genes at once to create a global picture of cell function.

How is transcriptome assembly quality measured?

The most basic metrics for transcriptome assemblies are aggregate and concern the size of the output. These include assembly size (in base pairs), percentage of reads assembled into contigs, and counts of contigs and singletons.

How can I improve my transcriptome assembly?

Best Practices for De Novo Transcriptome Assembly with Trinity

  1. 1 Consult with Informatics Group staff about study design.
  2. 2 Examine quality metrics for sequencing reads.
  3. 3 Removing erroneous k-mers from Illumina paired-end reads.
  4. 4 Discard read pairs for which one of the reads is deemed unfixable.

How does transcriptomics differ from genomics How are they similar?

Genomics provides an overview of the complete set of genetic instructions provided by the DNA, while transcriptomics looks into gene expression patterns.

Is transcriptome more effective than proteome?

Our data revealed a much higher dynamic within the proteome compared to the transcriptome. We cannot exclude that this higher dynamic is at least partly due to the different methods used for the respective transcriptomic and proteomic samples.

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