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velocyto-team / velocyto.R

RNA velocity estimation in R
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Error with read.smartseq2.bams #9

Closed abhaduri closed 6 years ago

abhaduri commented 6 years ago

When I run read.smartseq2.bams as noted in the documentation, I get the following error:

dat <- read.smartseq2.bams(files,"refFlat.txt",n.cores=40) reading gene annotation ... done ( 28051 genes) parsing exon information ... done reading in 2688 bam files ... done estimating gene counts ... done adjusting gene annotation based on expressed regions ... Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 'x' must be numeric

I am using GRCh38 and downloaded refFlat.txt from the UCSC browser, it has 11 columns. Any insight?

pkharchenko commented 6 years ago

Can you please provide more info. A stack trace would be a useful start. But most likely I’d have to debug and look at the variables to see what’s going on. Thanks, -peter.

On Dec 6, 2017, at 11:04 AM, abhaduri notifications@github.com wrote:

When I run read.smartseq2.bams as noted in the documentation, I get the following error:

dat <- read.smartseq2.bams(files,"refFlat.txt",n.cores=40) reading gene annotation ... done ( 28051 genes) parsing exon information ... done reading in 2688 bam files ... done estimating gene counts ... done adjusting gene annotation based on expressed regions ... Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 'x' must be numeric

I am using GRCh38 and downloaded refFlat.txt from the UCSC browser, it has 11 columns. Any insight?

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abhaduri commented 6 years ago

Let me know what else you may need- I am running this from R and got the following result from traceback:

traceback() 4: base::colSums(x, na.rm = na.rm, dims = dims, ...) 3: Matrix::colSums(do.call(rbind, parallel::mclapply(cdl, function(x) { ect <- table(c(x$exonstart, x$exonend)) fect <- rep(0, nrow(exons)) fect[as.integer(names(ect))] <- ect fect }, mc.cores = n.cores, mc.preschedule = T))) 2: Matrix::colSums(do.call(rbind, parallel::mclapply(cdl, function(x) { ect <- table(c(x$exonstart, x$exonend)) fect <- rep(0, nrow(exons)) fect[as.integer(names(ect))] <- ect fect }, mc.cores = n.cores, mc.preschedule = T))) 1: read.smartseq2.bams(files, "refFlat.txt", n.cores = 40)

pkharchenko commented 6 years ago

Is this mouse or human? Could you test if using the refFlat file from the chromaffin example gives a similar error? Does the format of the two files match? Thanks, -peter.

On Dec 6, 2017, at 11:27 AM, abhaduri notifications@github.com wrote:

Let me know what else you may need- I am running this from R and got the following result from traceback:

traceback() 4: base::colSums(x, na.rm = na.rm, dims = dims, ...) 3: Matrix::colSums(do.call(rbind, parallel::mclapply(cdl, function(x) { ect <- table(c(x$exonstart, x$exonend)) fect <- rep(0, nrow(exons)) fect[as.integer(names(ect))] <- ect fect }, mc.cores = n.cores, mc.preschedule = T))) 2: Matrix::colSums(do.call(rbind, parallel::mclapply(cdl, function(x) { ect <- table(c(x$exonstart, x$exonend)) fect <- rep(0, nrow(exons)) fect[as.integer(names(ect))] <- ect fect }, mc.cores = n.cores, mc.preschedule = T))) 1: read.smartseq2.bams(files, "refFlat.txt", n.cores = 40)

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abhaduri commented 6 years ago

This is human- can you post the refFlat from chromaffin? I got an error when untarring that download, unless I misunderstood the structure of that folder.

abhaduri commented 6 years ago

I was able to find the refFlat file- the formats match and when I just use that one (even if it is mouse, figured I could try it) it gives me the same errors. Any thoughts?