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

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

rna-seq transposable elements
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updated by h.mon h.mon • written by Elephantdumbo • Elephantdumbo

1 answer

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.

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written by h.mon h.mon

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

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written by Elephantdumbo • Elephantdumbo

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.

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written by h.mon h.mon

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