InsRegions

[PotapenkoEugene]

Thank you for great tool!

Can you explain output bed file:

chrUn 40491997 40492259 RLX 13 . FR=7;RR=6;InsRegion=40491614-40492275;FILTER=PASS

Can you explain what difference between first region and InsRegion? Which I need to use to calculate TEs length.

[VistaSohrab]

Thank you for your interest in the tool!
The entry in the output bed file reads as such: An RLX TE insertion site is found in chrUn at position 40491997-40492259 with a total of 13 reads supporting the insertion event. The first region, 40491997, is the start coordinate of the TE insertion site and the end coordinate is 40492259. InsRegion provides the genomic range that contains all the reads used in calling that TE insertion event, so in this case the 13 reads supporting the RLX insertion event spanned coordinates 40491614 to 40492275 in chrUn.
TEfinder was developed to detect new insertion events and report the genomic location of those insertion sites, so the reported coordinates were not used to determine TE length.