input file of bc_demultiplex

Question

[yueli7]

Hello,

I tried to use be_demultiplex from: https://github.com/yanailab/CEL-Seq-pipeline.

Thanks in advance for any great help!

Best,

Yue

li@-Desktp0xxx:~/CEL-Seq-pipeline-stable$ bc_demultiplex --out-dir test_out index sample_sheet_example.txt --not-gzip SRR9609653_1.fastq SRR9609653_2.fastq 

    usage: bc_demultiplex [-h] [--bc-index FILENAME] [--bc-seq-column N]
                      [--bc-index-used string] [--min-bc-quality N]
                      [--out-dir DIRNAME] [--is-gzip] [--not-gzip]
                      [--stats-file STATFILE] [--umi-start-position N]
                      [--umi-length N] [--bc-start-position N] [--bc-length N]
                      [--cut-length N] [--save-unknown-bc-fastq]
                      [--tagging-only] [--tag-to TAG_TO] [--verbose]
                      read1_fpath read2_fpath

    bc_demultiplex: error: unrecognized arguments: SRR9609653_1.fastq SRR9609653_2.fastq

[ATpoint]

bc_demultiplex --out-dir test_out index sample_sheet_example.txt --not-gzip SRR9609653_1.fastq SRR9609653_2.fastq

There is no option index according to the listed parameters and if it exists then either as -index or --index. I guess you have to write --bc-index, in any case your command line is probably wrong, check with the manual and find out which parameters are incorrect. Since the command line is wrong the files at the end of the line are not interpreted correctly and therefore this error is probably thrown.

[yueli7]

Hello, ATpoint,

Still have not figure it out. But your answer seems correct!

Thank you!

Best,

Yue

[GenoMax]

I tried to use be_demultiplex from

Did you modify this config file for your local setup: https://github.com/yanailab/CEL-Seq-pipeline/blob/stable/config_file_example.txt

[yueli7]

Hello, genomax,

Thank you so much for your replying.

Still working on it and not worked it out!

Best,

Yue