long reads about sierra

[rj-patrick]

Hi @ashokpatowary,

I haven't come across this error before, and it's hard to judge the cause without being able to replicate the error. I doubt that the size of your data set is the problem, but there could be something strange with the format of your peaks if you are using long read data. Would you be able to show some examples of the peak feature annotations? e.g. if using a Seurat object by running head(Tool(peaks.seurat, "Sierra"), n=20). Also, I assume you were able to run the Vignette example without error?

Cheers,
Ralph

[ashokpatowary]

Hi @reprobate

Thanks for your response. Yes I can run the example. here is the outcome from head(Tool(peaks.seurat, "Sierra"), n=20).

UTR3 UTR5 intron exon FeaturesCollapsed Gene_name start end chr strand pA_motif pA_stretch Junctions Gene_part Peak_number
TSPAN6:chrX:99890574-99891803:-1 NA NA YES YES intron;exon TSPAN6 99890574 99891803 chrX - FALSE FALSE across-junctions TSPAN6:4 Peak4
TSPAN6:chrX:99884321-99888504:-1 NA NA YES YES intron;exon TSPAN6 99884321 99888504 chrX - FALSE FALSE across-junctions TSPAN6:2 Peak2
TSPAN6:chrX:99883514-99885793:-1 NA NA YES YES intron;exon TSPAN6 99883514 99885793 chrX - FALSE FALSE across-junctions TSPAN6:1 Peak1
TSPAN6:chrX:99884324-99884714:-1 NA NA YES exon TSPAN6 99884324 99884714 chrX - FALSE FALSE no-junctions TSPAN6:3 Peak3
DPM1:chr20:49551114-49575092:-1 NA NA YES YES intron;exon DPM1 49551114 49575092 chr20 - FALSE FALSE across-junctions DPM1:1 Peak1
DPM1:chr20:49551295-49562420:-1 NA NA YES YES intron;exon DPM1 49551295 49562420 chr20 - FALSE FALSE across-junctions DPM1:2 Peak2
DPM1:chr20:49551322-49551658:-1 NA NA YES exon DPM1 49551322 49551658 chr20 - FALSE FALSE no-junctions DPM1:3 Peak3
LAS1L:chrX:64737214-64754655:-1 NA NA YES YES intron;exon LAS1L 64737214 64754655 chrX - FALSE TRUE across-junctions LAS1L:2 Peak2
LAS1L:chrX:64753523-64754655:-1 NA NA YES YES intron;exon LAS1L 64753523 64754655 chrX - FALSE FALSE across-junctions LAS1L:5 Peak5
LAS1L:chrX:64736518-64754655:-1 NA NA YES YES intron;exon LAS1L 64736518 64754655 chrX - FALSE FALSE across-junctions LAS1L:1 Peak1
LAS1L:chrX:64743522-64749717:-1 NA NA YES YES intron;exon LAS1L 64743522 64749717 chrX - FALSE FALSE across-junctions LAS1L:3 Peak3
LAS1L:chrX:64744065-64744457:-1 NA NA YES YES intron;exon LAS1L 64744065 64744457 chrX - FALSE FALSE across-junctions LAS1L:4 Peak4
ANKIB1:chr7:91875288-91957189:1 NA NA YES YES intron;exon ANKIB1 91875288 91957189 chr7 + FALSE FALSE across-junctions ANKIB1:1 Peak1
CYP51A1:chr7:91763310-91763934:-1 NA NA YES YES intron;exon CYP51A1 91763310 91763934 chr7 - FALSE FALSE no-junctions CYP51A1:1 Peak1
BAD:chr11:64037302-64052176:-1 NA NA YES YES intron;exon BAD 64037302 64052176 chr11 - TRUE FALSE across-junctions BAD:1 Peak1
BAD:chr11:64037675-64052176:-1 NA NA YES YES intron;exon BAD 64037675 64052176 chr11 - FALSE FALSE across-junctions BAD:2 Peak2
BAD:chr11:64051807-64052176:-1 NA NA YES YES intron;exon BAD 64051807 64052176 chr11 - FALSE FALSE across-junctions BAD:3 Peak3
CD99:chrX:2609228-2659350:1 NA NA YES YES intron;exon CD99 2609228 2659350 chrX + TRUE FALSE across-junctions CD99:1 Peak1
CD99:chrX:2609228-2637704:1 NA NA YES YES intron;exon CD99 2609228 2637704 chrX + FALSE FALSE across-junctions CD99:2 Peak2
CD99:chrX:2658834-2659350:1 NA NA YES exon CD99 2658834 2659350 chrX + TRUE FALSE no-junctions CD99:3 Peak3

[rj-patrick]

Thanks for that. It's not obvious that there is anything that would cause an error, though it's possible that there are just some peaks that are causing a problem. If you were to take subsets of your data are you able to reproduce the error? If you had a small subset reproducing the error that you could send that would help us to diagnose the problem.

[ashokpatowary]

Hi @reprobate

I will try with a subset of the data. But I came across the same error even if I change the cell population to a different one.

[ashokpatowary]

Hi @reprobate

I tried it on a small dataset and still the same error.

[rj-patrick]

Hi @ashokpatowary,

Thanks for that. Would it be possible to share a small dataset with us that replicates the error?

[ashokpatowary]

@reprobate

Sure. What all files will you need and can you share your email please?

[rj-patrick]

If you could just send a peaks Seurat object that you're getting the error on, and the DUTest command you are running that would be most helpful. My email is [email protected]

[ashokpatowary]

Hi @reprobate ,

I just send you the mail. Thanks