Unplaced sequences

[vappiah]

Hi @malonge . I run ragtag and identified some sequences are unplaced. Is there anyway to find out which sequences were unplaced? I would like to do further analysis on these unplaced sequences. If not then I will just write a script to manually check. Thanks

[malonge]

Hi there,

There are two main ways to tell if a sequence was unplaced. First of all, an unplaced sequence will not appear in the first column of ragtag.confidence.txt. Also, unplaced sequences, by default, will be assigned their original header in the final scaffolds output (+ "_RagTag" suffix if using -u). If using -C, it will be placed in chromosome zero, and you can find all query sequences in chromosome 0 by looking at ragtag.scaffolds.agp.