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campbio / scruff

Single Cell RNA-seq UMI Filtering Facilitator
http://bioconductor.org/packages/scruff/
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Error in if (ncol(sce) != length(cellPerWell) & length(cellPerWell) != : argument is of length zero #184

Closed parichitran closed 2 years ago

parichitran commented 2 years ago

Greetings, I have a CEL-seq data incorpatated with umi.The following are the details of my reads Reads were already demultiplexed to indivdual cell Fastq reads READ-1 =8bp(cell barcode)+5bp(umi) READ-2= (47bp) Lets say if allign this Fastq and created a BAM file.How i can get deduplicated umi counts with scruff. My case i also needed a deduplicated BAM file too.

I already tried to count umi using my BAM file genrated from STAR alligner i got the above error

zhewa commented 2 years ago

Hi @parichitran Suppose you have a vector called PATH_TO_FASTQ in R that contains the paths to individual demultiplexed FASTQ files, and a variable called PATH_TO_GTF which is the path to Rsubread index. The minimal command to generate BAM files and a count matrix would be:

library(SingleCellExperiment)
library(scruff)

sce <- SingleCellExperiment(colData = DataFrame(fastq_path = PATH_TO_FASTQ))

scealign <- alignRsubread(sce, index = PATH_TO_RSUBREAD_INDEX)
scecount <- countUMI(scealign, reference = PATH_TO_GTF)