I am new to the TE field and I would really appreciate if you could help me with the interpretation of the output files. I work on human samples (on a specific cell type; sequenced with ONT) from before and after treatment in which active mobile element content is not at all understood but it is human genome so can I consider it as "not at all understood"? I tried either with -e teref.ont.human.fa or -e noneand also --non ref_ nonref.collection.hg19.bed. with different outputs.
1) Do we need to specifiy a --ref_ genome when --non ref is specified?
2) Can we run tldr with -e nonref.collection.hg19.bedor it has to go with --non ref ?
3) The outputs of -e teref.ont.human.fa from before and after treatment differs, some insertions disappear and while some few are new. Is this due to the analysis itself or can I interpret it as insertions that have disappeared/appeared because of the treatment?
Hi Adam,
I am new to the TE field and I would really appreciate if you could help me with the interpretation of the output files. I work on human samples (on a specific cell type; sequenced with ONT) from before and after treatment in which active mobile element content is not at all understood but it is human genome so can I consider it as "not at all understood"? I tried either with
-e teref.ont.human.faor-e noneand also--non ref_ nonref.collection.hg19.bed. with different outputs.1) Do we need to specifiy a
--ref_ genomewhen--non refis specified? 2) Can we run tldr with-e nonref.collection.hg19.bedor it has to go with--non ref? 3) The outputs of-e teref.ont.human.fafrom before and after treatment differs, some insertions disappear and while some few are new. Is this due to the analysis itself or can I interpret it as insertions that have disappeared/appeared because of the treatment?Appreciate any help! Thank You!!