Unable to Generate Motif class for zebrafish scATAC data using Signac package.

Question

[vetrosh]

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?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted.

It looks like you used the quote (the one with the double quotes on it) option or pasted content with leading > symbols - that tends to wreck all formatting. Please edit your post and re-paste the content but this time use the code formatting option. Even if your text contains leading > symbols, code formatting will handle them properly.