Indexing reads from long range PCR
I have some trouble to index my reads from a long range PCR approach. I got a set of reads from a 6 kb fragment and one from a 12 kb fragment making for a whole mitochondrial genome. However, if I want to index my reads --- let's say from the short fragment (6 kb) --- 0 reads can be indexed, it seems like that my paired-end reads from Illumina (Nextera XT library kit) won't be processed because ORG.Asm cannot find corresponding ids (when using '--check-pairing'). Might there be a way to circumvent this issue?