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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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How can I obtain the location where reads map to TEs #44

Closed CPTPaso closed 4 years ago

CPTPaso commented 4 years ago

Hi,

is there a way to check the genomic location where the TEs identified by SalmonTE are located? Then I could easily load the bams into IGV and validate SalmonTE findings and would not have to run a RT-qPCR in the first place.

Thanks for your help!

hyunhwan-jeong commented 4 years ago

Hi @CPTPaso, there a couple of ways you can lookup the potential loci:

  1. Using databases like dfam, RepeatMasker, or RepeatBrowser
  2. You can blat with the TE sequence.

Please be aware that SalmonTE only quantifies overall TE abundances can't extract the exact locus. Please refer #42 - there a discussion regarding this matter.

Best,

Hyun-Hwan Jeong