Hi, I am analyzing zebrafish scATAC data using Signac package. The package does not allow me to create motif class. It gives me the following error after running AddMotif function. `ATAC <- AddMotifs(
- object = ATAC,
- genome = BSgenome.Drerio.UCSC.danRer11,
- pfm = pfm
- )`
Building motif matrix Warning in CreateMotifMatrix(features = object, pwm = pfm, genome = genome, : Not all seqlevels present in supplied genome Finding motif positions Creating Motif object Error in SetAssayData.ChromatinAssay(object = object, slot = "motifs", : No features in common between the ChromatinAssay and Motif objects In addition: Warning messages: 1: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
- in 'x': chrM, chr1_KZ114834v1_alt, chr1_KZ114835v1_alt, chr1_KZ114836v1_alt, chr1_KZ114837v1_alt, chr1_KZ114838v1_alt, chr1_KZ114839v1_alt, chr1_KZ114840v1_alt, chr1_KZ114841v1_alt, chr1_KZ114842v1_alt, chr1_KZ114843v1_alt, chr1_KZ114844v1_alt, chr1_KZ114845v1_alt, chr1_KZ114846v1_alt, chr1_KZ114847v1_alt, chr1_KZ114997v1_alt, chr1_KZ114998v1_alt, chr1_KZ114999v1_alt, chr1_KZ115000v1_alt, chr1_KZ115001v1_alt, chr1_KZ115002v1_alt, chr1_KZ115003v1_alt, chr1_KZ115004v1_alt, chr1_KZ115005v1_alt, chr1_KZ115006v1_alt, chr1_KZ115007v1_alt, chr1_KZ115008v1_alt, chr1_KZ115009v1_alt, chr1_KZ115010v1_alt, chr1_KZ115011v1_alt, chr1_KZ115012v1_alt, chr1_KZ115013v1_alt, chr1_KZ115014v1_alt, chr1_KZ115015v1_alt, chr1_KZ115016v1_alt, chr1_KZ115017v1_alt, chr1_KZ115018v1_alt, chr1_KZ115019v1_alt, chr1_KZ115020v1_alt, chr1_KZ115021v1_alt, chr1_KZ115022v1_alt, chr1_KZ115023v1_alt, chr1_KZ115024v1_alt, chr1_KZ115025v1_alt, chr1_KZ115 [... truncated] 2: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
- in 'x': chrM, chr1_KZ114834v1_alt, chr1_KZ114835v1_alt, chr1_KZ114836v1_alt, chr1_KZ114837v1_alt, chr1_KZ114838v1_alt, chr1_KZ114839v1_alt, chr1_KZ114840v1_alt, chr1_KZ114841v1_alt, chr1_KZ114842v1_alt, chr1_KZ114843v1_alt, chr1_KZ114844v1_alt, chr1_KZ114845v1_alt, chr1_KZ114846v1_alt, chr1_KZ114847v1_alt, chr1_KZ114997v1_alt, chr1_KZ114998v1_alt, chr1_KZ114999v1_alt, chr1_KZ115000v1_alt, chr1_KZ115001v1_alt, chr1_KZ115002v1_alt, chr1_KZ115003v1_alt, chr1_KZ115004v1_alt, chr1_KZ115005v1_alt, chr1_KZ115006v1_alt, chr1_KZ115007v1_alt, chr1_KZ115008v1_alt, chr1_KZ115009v1_alt, chr1_KZ115010v1_alt, chr1_KZ115011v1_alt, chr1_KZ115012v1_alt, chr1_KZ115013v1_alt, chr1_KZ115014v1_alt, chr1_KZ115015v1_alt, chr1_KZ115016v1_alt, chr1_KZ115017v1_alt, chr1_KZ115018v1_alt, chr1_KZ115019v1_alt, chr1_KZ115020v1_alt, chr1_KZ115021v1_alt, chr1_KZ115022v1_alt, chr1_KZ115023v1_alt, chr1_KZ115024v1_alt, chr1_KZ115025v1_alt, chr1_KZ115 [... truncated] 3: In rownames(x = object) == rownames(x = new.data) : longer object length is not a multiple of shorter object length
I used ensemble genome and annotation files during cellranger-atac count. Can anyone help me to figure out this?
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