QC a crypto run output by the novoalign+htseq pipeline
novoalignPipelineQC.Rdcoverage and log2cpm are both over the annotated CDS
Usage
novoalignPipelineQC(
meta_df,
pipeline_output_dirpath,
annote_obj_path,
markers = c("NAT", "G418"),
bam_suffix = "_sorted_aligned_reads_with_annote.bam",
novolog_suffix = "_novoalign.log",
exon_counts_suffix = "_read_count.tsv",
cds_counts_suffix = "_read_count_cds.tsv",
num_nodes = 10
)Arguments
- meta_df
metadata for the samples you'd like to QC. note that these must be included in the pipeline_output_dirpath
- pipeline_output_dirpath
path to the directory which stores the subdirectories align, count and logs, eg /mnt/scratch/rnaseq_pipeline/pipeline_out/run_5500
- annote_obj_path
path to an annotation file parsed by rtracklayer::import
- markers
a list of markers. must be in the counts and genome annotations. default is c("NAT", "G418")
- bam_suffix
suffix appended to the bam files. default is "_sorted_aligned_reads_with_annote.bam"
- novolog_suffix
suffix appended to log files. default is "_novoalign.log"
- exon_counts_suffix
suffix appended to exon count files. default is '_read_count.tsv'
- cds_counts_suffix
suffix appended to cds count files. default is '_read_count.tsv'
- num_nodes
number of cpus(by slurm definition)/threads(on your local). the argument in the parallel function is nnodes, hence the name of the argument. Default is 10