PICARD COLLECTRNASEQMETRICS¶
Run picard CollectRnaSeqMetrics to generate QC metrics for RNA-seq data.
URL: https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics
Example¶
This wrapper can be used in the following way:
rule alignment_summary:
input:
# BAM aligned, splicing-aware, to reference genome
bam="mapped/a.bam",
# Reference genome
#ref="ref.fasta",
# Annotation file containing transcript, gene, and exon data
refflat="annotation.refFlat",
output:
"results/a.rnaseq_metrics.txt",
params:
# strand is optional (defaults to NONE) and pertains to the library preparation
# options are FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND, and NONE
strand="NONE",
# optional additional parameters, for example,
extra="--VALIDATION_STRINGENCY STRICT",
log:
"logs/picard/rnaseq-metrics/a.log",
resources:
mem_mb=1024,
wrapper:
"v1.12.2/bio/picard/collectrnaseqmetrics"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The extra param allows for additional program arguments.
- –TMP_DIR is automatically set by resources.tmpdir
Software dependencies¶
picard=2.27
snakemake-wrapper-utils==0.1.3
Input/Output¶
Input:
- BAM file of RNA-seq data aligned to genome
- REF_FLAT formatted file of transcriptome annotations
- reference FASTA (optional)
Output:
- RNA-Seq metrics text file
Authors¶
- Brett Copeland
- Filipe G. Vieira
Code¶
__author__ = "Brett Copeland"
__copyright__ = "Copyright 2021, Brett Copeland"
__email__ = "brcopeland@ucsd.edu"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell()
strand = snakemake.params.get("strand", "NONE")
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
ref = snakemake.input.get("ref", "")
if ref:
ref = f"--REFERENCE_SEQUENCE {ref}"
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"picard CollectRnaSeqMetrics"
" {java_opts} {extra}"
" --INPUT {snakemake.input.bam}"
" {ref}"
" --REF_FLAT {snakemake.input.refflat}"
" --STRAND_SPECIFICITY {strand}"
" --TMP_DIR {tmpdir}"
" --OUTPUT {snakemake.output}"
" {log}"
)