Hi,

I am trying to scaffold 97 contigs from C. elegans into chromosomes. After blasting my contigs to the reference, I am running the chromosomer fragmentmap command:

chromosomer fragmentmap output/alignment/celegans/ref/pacbio/contigs/canu/blastn/bristol.txt 1000 output/assembly/celegans/canu/bristol/celegans.contigsChromosomer.fasta output/alignment/celegans/ref/pacbio/contigs/canu/blastn/map.txt
2017-08-30 17:30:13 - 59 mapped fragments of total length 58925391 bp
2017-08-30 17:30:13 - 38 unlocalized fragments of total length 43828989 bp
2017-08-30 17:30:13 - 0 unplaced fragments of total length 0 bp
2017-08-30 17:30:13 - 6 chromosomes formed
2017-08-30 17:30:13 - 59000 bp of gaps inserted

These contigs all have a pretty good primary alignment to the reference since they come from the reference strain. Therefore, I have quite high expectations in terms of forming complete chromosomes. Do you know what the difference is between the unlocalized and the unplaced fragments?

Thanks.

Best, C.