NextClone and CloneDetective: An Integrated Nextflow Pipeline and R Package for Clonal Barcode Extraction and Quantification

BAM file (chunk 1-25 of 50) for the scRNAseq data required to replicate the analyses presented at: https://phipsonlab.github.io/NextClone-analysis/.

Chunk 26-50 can be downloaded from https://zenodo.org/uploads/10129625

The original BAM file was too big to fit in an entry. Thus it was split into 50 using picard:

SplitSamByNumberOfReads -I possorted_genome_bam.bam -O split_sam/ -N_FILES 50 --CREATE_MD5_FILE

Before re-running all the analyses in https://phipsonlab.github.io/NextClone-analysis/, make sure you merge all 50 chunks first using picard (change xxx to point to the directory storing all the 50 chunks you have downloaded):

outdir="xxx"

args=""

# Loop through each BAM file

for file in ${outdir}/*.bam; do

    args+="-I $file "

done

# Do the actual merging

MergeSamFiles $args -O $outdir/merged_v2/merged_bam_v2.bam --USE_THREADING --CREATE_MD5_FILE

Picard can be downloaded from: https://github.com/broadinstitute/picard