genomeAnnotation$chromSizes are blank

[tao-bioinfo]

I created a GRanges object called chrsize_gr:

> chrsize_gr
GRanges object with 2190 ranges and 0 metadata columns:
             seqnames      ranges strand
                <Rle>   <IRanges>  <Rle>
     [1]          A01 1-117710661      *
     [2]          A02 1-108049532      *
     [3]          A03 1-113014280      *
     [4]          A04  1-85114396      *
     [5]          A05 1-109365994      *
     ...          ...         ...    ...
  [2186]  Scaffold827     1-25913      *
  [2187] Scaffold1545     1-40954      *
  [2188] Scaffold3346      1-6326      *
  [2189] Scaffold1026      1-7792      *
  [2190] Scaffold3053     1-30723      *
  -------
  seqinfo: 2190 sequences from an unspecified genome

I also created a BSgenome object called BSgenome.Ghir.HAU.v1

> BSgenome.Ghir.HAU.v1
cotton genome:
# organism: Gossypium hirsutum (cotton)
# provider: HAU
# provider version: v1
# release date: 2019
# release name: 2019
# 2190 sequences:
#   A01                          A02
#   A03                          A04
#   A05                          A06
#   A07                          A08
#   A09                          A10
#   ...                          ...
#   Scaffold1884                 Scaffold3335
#   Scaffold866                  Scaffold1189
#   Scaffold1576                 Scaffold827
#   Scaffold1545                 Scaffold3346
#   Scaffold1026                 Scaffold3053
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)

Then I build genomeAnnotation:

> genomeAnnotation = createGenomeAnnotation(genome = BSgenome.Ghir.HAU.v1, chromSizes = chrsize_gr)
Getting genome..
Getting chromSizes..
Getting blacklist..
Blacklist not downloaded! Continuing without, be careful for downstream biases..
> genomeAnnotation
List of length 3
names(3): genome chromSizes blacklist

However the genomeAnnotation$chromSizes are blank

> genomeAnnotation$genome
[1] "BSgenome.Ghir.HAU.v1"

> genomeAnnotation$chromSizes
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: no sequences
> help(createGenomeAnnotation)

What's the problem?

[rcorces]

Presumably you need to set filter=FALSE in createGenomeAnnotation() because none of your chromosomes represent standard chromosomes.
https://www.archrproject.com/reference/createGenomeAnnotation.html

[tao-bioinfo]

Fixed