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LuyiTian / scPipe

a pipeline for single cell RNA-seq data analysis
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sc_trim_barcode problem in single-end data #138

Open MiladAD123NGS opened 2 years ago

MiladAD123NGS commented 2 years ago

hello dear developers of scPipe

I have an issue in running sc_trim_barcode at the first step of scPipe pipeline for single-end data. Running sc_trim_barcode like the command below, resulted in " not implemented. " error.

My command is:

sc_trim_barcode(file.path(data_dir, "combined.fastq"),
                fq_R1, r2 = NULL,
                read_structure = list(bs1 = 0, bl1 = 16, us = 16, ul = 10),
                filter_settings = list(rmlow = TRUE, rmN = TRUE, minq = 20, numbq = 2))

Error message is:

Error in sc_trim_barcode(file.path(data_dir, "combined.fastq"), fq_R1,  : 
  not implemented.

I need an immediate answer if possible. thanks in advance for your help

LuyiTian commented 2 years ago

you need paired-end read as input so two fastq file.