blacklist doesn't work

[esroom]

Hi, thanks for developing this amazing tool.

I'm confused about the blacklist used in the default hg38 genome! According to the manual, the blacklist was precompiled into the hg38 genome by using addArchRGenome("hg38"). And I could see it by using getGenomeAnnotation(proj)$blacklist. Here is the result:

But when looking into the TileMatrix using mat <- getMatrixFromProject(proj, binarize = TRUE, useMatrix = "TileMatrix"), the ranges in the blacklist were inside rowData(mat).

Also this happened in the PeakSet called by addReproduciblePeakSet.

I used ArchR 1.0.1. I wondered if this is normal, or the blacklist should be removed by some settings?

[rcorces]

I am unable to recapitulate this behavior on release_1.0.2 using the tutorial code and data. When I retrieve a peak matrix, it does not have ranges overlapping the blacklisted regions.

> getBlacklist(projHeme5)
GRanges object with 1569 ranges and 2 metadata columns:
         seqnames              ranges strand | Buenrostro    Encode
            <Rle>           <IRanges>  <Rle> |  <logical> <logical>
     [1]     chr1            1-750100      * |       TRUE      TRUE
     [2]     chr1       814501-845200      * |      FALSE      TRUE
     [3]     chr1     2052401-2056000      * |      FALSE      TRUE
     [4]     chr1     2582801-2693900      * |      FALSE      TRUE
     [5]     chr1     4362201-4364300      * |      FALSE      TRUE
     ...      ...                 ...    ... .        ...       ...
  [1565]     chrX 154528901-154616300      * |      FALSE      TRUE
  [1566]     chrX 155038501-155270500      * |      FALSE      TRUE
  [1567]     chrY    7432701-13491000      * |      FALSE      TRUE
  [1568]     chrY   13633401-14289000      * |      FALSE      TRUE
  [1569]     chrY   28783401-59373500      * |      FALSE      TRUE
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

> peakSE <- getMatrixFromProject(ArchRProj = projHeme5, useMatrix = "PeakMatrix")
ArchR logging to : ArchRLogs/ArchR-getMatrixFromProject-213b8e14f4548-Date-2021-11-29_Time-09-05-42.log
If there is an issue, please report to github with logFile!
2021-11-29 09:05:45 : Organizing colData, 0.054 mins elapsed.
2021-11-29 09:05:45 : Organizing rowData, 0.055 mins elapsed.
2021-11-29 09:05:45 : Organizing rowRanges, 0.055 mins elapsed.
2021-11-29 09:05:45 : Organizing Assays (1 of 1), 0.055 mins elapsed.
2021-11-29 09:05:45 : Constructing SummarizedExperiment, 0.058 mins elapsed.
2021-11-29 09:05:47 : Finished Matrix Creation, 0.084 mins elapsed.

> rowRanges(peakSE)
GRanges object with 143400 ranges and 1 metadata column:
           seqnames              ranges strand |     idx
              <Rle>           <IRanges>  <Rle> | <array>
       [1]     chr1       752502-753002      * |       1
       [2]     chr1       762685-763185      * |       2
       [3]     chr1       779917-780417      * |       3
       [4]     chr1       793283-793783      * |       4
       [5]     chr1       801006-801506      * |       5
       ...      ...                 ...    ... .     ...
  [143396]     chrX 154840785-154841285      * |    3413
  [143397]     chrX 154841356-154841856      * |    3414
  [143398]     chrX 154842430-154842930      * |    3415
  [143399]     chrX 154862053-154862553      * |    3416
  [143400]     chrX 154997960-154998460      * |    3417
  -------
  seqinfo: 23 sequences from an unspecified genome; no seqlengths