vizulization of the mapping total RNA-seq data to a consensus sequence of a transposable element

Question

[Elephantdumbo]

Hello, is there a way i could visualize the mapping of the cDNA to a reference sequence i provide of a transposable element ? I am trying to improve an annotation of a certain element and mapping RNA can help with that because it is a reterotranspon and has an RNA intermediate

Thank you

Answer 1

[h.mon]

How did you align the data? What is the format of the alignment? Probably Tablet, IGV, IGB, Artemis and other genome browsers can do what you want.

[Elephantdumbo]

i used bowtie2 and output bam. should i use salmon or kallisto better ? I think IGV is good

[h.mon]

If you expect the TE have introns, it would be better to use hisat2, star, gsnap, bbmap, among many other splice-aware aligners. Otherwise, bowtie2 is just fine.