-
Notifications
You must be signed in to change notification settings - Fork 0
Running RRBS pipeline
Welcome to the motrpac-rrbs-pipeline wiki!
- Optimized memory requirements for processing RRBS pass samples
default parameters
memory = 40
disk_space = 150
threads =6
preTrimFastQC
memory=memory,
disk_space=disk_space,
num_threads=1
attachUMI
memory=40,
disk_space=disk_space,
num_threads=8
trimgalore
memory=40,
disk_space=disk_space,
num_threads=1
NuGen specific diversity adapaters trimmed
` memory=memory,`
`disk_space=disk_space,`
`num_threads=1,`
`num_preempt=num_preempt,`
FastQC ran on post trimming reads
`memory=memory,`
`disk_space=disk_space,`
`num_threads=1,`
`num_preempt=num_preempt,`
multiQC
memory=memory,
`disk_space=disk_space,`
`num_threads=1,`
Align trimmed reads to species of interest
memory=100,
`disk_space=200,`
`num_threads=12,`
`num_preempt=0,`
`bismark_multicore=3,`
Align trimmed reads to lambda for control
memory=100
`disk_space=200`
`num_threads=12`
`num_preempt=0`
Tag UMI duplications in sample and spike-in
`memory=memory,`
`disk_space=disk_space,`
`num_threads=6,`
Remove PCR Duplicates from sample
`memory=30,`
`disk_space=200,`
`num_threads=1,`
Remove PCR Duplicates from Lambda phage spike in
`memory=memory,`
`disk_space=disk_space,`
`num_threads=1,`
Quantify Methylation for sample
`memory=60,`
`disk_space=200,`
`num_threads=16,`
Quantify Methylation for Lambda control spike in
`memory=60,`
`disk_space=200,`
`num_threads=16,`
Align trimGalore trimmed reads to phix genome using bowtie
`memory=40,`
`disk_space=200,`
`num_threads=10,`
`num_preempt=0`
Compute % mapped to chromosomes and contigs
`num_threads=8,`
`memory=30,`
`disk_space=200,`
`num_preempt=0,`
Collect required QC Metrics from reports
`memory=20,`
`disk_space=50,`
`num_threads=4,`
`num_preempt=0`
- Datasets to process
-
gs://motrpac-portal-transfer-sinai/RRBS/PASS1A/batch1_20190528/fastq_raw -
gs://motrpac-portal-transfer-sinai/RRBS/PASS1A/batch2_20190706/fastq_raw
Output location
gs://rna-seq_araja/rrbs/PASS1A/reprocessed/
`