Closed aseetharam closed 9 years ago
Ah, I see "reads mapping to different contigs' is 0! Sorry, my bad. Please close the issue!
Hi,
BESST uses information between genomic read pairs to scaffold contigs. BESST_rna is a modified version of BESST where RNA-seq can be used to scaffold (we don't know the genomic distance between RNA read pairs, it depends on the intron size). However, in both cases the softwares need to know what reads/segments belong together in order to scaffold. BESST and BESST_rna extracts this information from the bam file, so the segments needs to be aligned in a way such that pairs are recognised. Hope this helps your issue!
I was trying to test this script and ran it on my dataset (as given in your readme), by I got this error:
Do you know if I did something wrong? FYI, I used trinity de novo assembled transcripts and mapped to my assembled genome using GMAP (default parameters).
I greatly appreciate any help. Thanks!