phasegenomics / FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
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haplotig header suffix. Does the order matter? #72

Closed Juke34 closed 4 years ago

Juke34 commented 4 years ago

I need to convert headers modified by a third-party tool in a proper way to feed falcon-phase. I was wondering if the suffix numbering in the haplotig header has an important meaning?

e.g my primary contig:

>000370F

my haplotigs

>000370F_001
>000370F_002
>000370F_003

Does the order 001, 002, 003 reflects any order in the primary contig, like alignment order? i.e must it be like that (case1):

primary  -------------------------------------------------------------------------

haoplotig   ---------------      -------------------        ------------------------
              001                           002                          003

or it does not matter and can be any order like (case2):

primary   -------------------------------------------------------------------------

haoplotig   ---------------      -------------------        ------------------------
               003                           001                    002
skingan commented 4 years ago

The suffix on the haplotig name does not indicate order.