Consideration of ERV splicing events.

mlbendall / telescope

Quantification of transposable element expression using RNA-seq

MIT License

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Consideration of ERV splicing events. #14

Open yyoshiaki opened 4 years ago

yyoshiaki commented 4 years ago

Hi,

I would like to ask about the splicing events of ERV. mRNAs from ERV are sometimes spliced, but in the article, you executed telescope for the bam files generated by bowtie2 which doesn't consider the splicing. When we switch the aligner from bowtie2 to hisat2 or STAR, will telescope work well theoretically?

millerh1 commented 4 years ago

I also have this question. Couldn't STAR be used instead of bowtie2?

lennartraman commented 2 years ago

Any update on this?