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nerettilab / RepEnrich2

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
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Keep alignments to metagenome #17

Closed adomingues closed 4 years ago

adomingues commented 4 years ago

Hi @nskvir this basically to reboot an issue from V1 because it might have been solved now in `repEnrich2 but I could not find which are the major differences with the previous version.

Basically what I want to know is if this new version keeps the alignments to repeat consensus (which v1 didn't), or if repConsensus is still the way to go?

Just as a background, I am working on a project where we want to know if

  1. there is change in bulk expression of TE; and
  2. if there is loss/gain of strand bias.

For 2 I definitely need the alignments, therefore the question.

Cheers.

nskvir commented 4 years ago

Hi there,

Apologies for the delayed reply - occasionally the notifications don't show up in my inbox when an issue is posted. The main difference between version 1 and 2 is a change of aligners used (from Bowtie1 to Bowtie2), but aside from that they behave in the same manner (meaning the alignments to pseudo-genomes are unfortunately not currently preserved).

Best, Nick