Problem with command

[ollieeknight]

Heya,

This tool looks really cool. I'm trying to run it on some 10x scATAC data generated with cellranger atac 2.0.1. here is the command and directory I'm trying to run it in, and error I encounter:

~/scratch/ngs/data $ java -Xmx48g -jar ~/work/bin/telomemore/telomemore.jar output.csv -countkmer -filterbc outs/sample/outs/filtered_peak_bc_matrix/barcodes.tsv -10xbampe outs/sample/outs/possorted_bam.bam
Will look for repeats of -filterbc * 5
Unknown parameter: outs/sample/outs/filtered_peak_bc_matrix/barcodes.tsv

~/scratch/ngs/data$ ls outs/sample/*
outs/sample/sample.mri.tgz

outs/sample/outs:
analysis       cut_sites.bigwig         filtered_peak_bc_matrix.h5  fragments.tsv.gz.tbi  peaks.bed          possorted_bam.bam.bai  raw_peak_bc_matrix.h5  summary.csv   web_summary.html
cloupe.cloupe  filtered_peak_bc_matrix  fragments.tsv.gz            peak_annotation.tsv   possorted_bam.bam  raw_peak_bc_matrix     singlecell.csv         summary.json

Thank you!

[AidanJFlynn]

I'm not affiliated with the tool but it looks like you have not specified the kmer to count so it's picking up the next parameter as the kmer and then falling out of sync:
java -jar ~/work/bin/telomemore/telomemore.jar output.csv -filterbc outs/sample/outs/filtered_peak_bc_matrix/barcodes.tsv -countkmer CCCTAA -10xbampe outs/sample/outs/possorted_bam.bam