04. Conversion of CRAM‐to‐BAM

It may happen that you already own aligned files but in .cram format rather than .bam. However, the ChIP-seq analyses pipeline works only with .bam files. Therefore, to convert the crams to bams you can use the mini-pipeline provided in this repository.

snakemake \
--cores 10 \
-s </target/folder>/SPACCa/workflow/SPACCA_cramToBam.snakefile \
--config \
cram_directory="/path/to/input/cram_folder" \
bam_out_directory="/path/to/output/bam_folder" \
genome_fasta="/path/to/genome.fa"

NOTE: remember that the genome used for the conversion must match with the one used to generate the crams.