Changes between Version 8 and Version 9 of SOPs/RRBS
- Timestamp:
- 08/08/24 11:47:15 (5 months ago)
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SOPs/RRBS
v8 v9 13 13 14 14 {{{ 15 bsub bismark_genome_preparation --bowtie2 /path/to/organism/reference/assembly/fasta 15 sbatch --partition=20 --job-name=bismark --mem=32G --wrap "bismark_genome_preparation --bowtie2 /path/to/organism/reference/assembly/fasta" 16 16 }}} 17 17 … … 24 24 25 25 {{{ 26 bsub trim_galore --paired --rrbs --fastqc -o trimmedReads /path/to/raw/data/reads_1.fq.gz /path/to/raw/data/reads_2.fq.gz 26 sbatch --partition=20 --job-name=TG --mem=32G --wrap "trim_galore --paired --rrbs --fastqc -o trimmedReads /path/to/raw/data/reads_1.fq.gz /path/to/raw/data/reads_2.fq.gz" 27 27 }}} 28 28 … … 33 33 34 34 {{{ 35 bsub bismark --genome /nfs/genomes/myOrganism/bowtie/ -1 trimmedReads_1.fq.gz -2 trimmedReads_2.fq.gz 35 sbatch --partition=20 --job-name=bismark--mem=32G --wrap "bismark --genome /nfs/genomes/myOrganism/bowtie/ -1 trimmedReads_1.fq.gz -2 trimmedReads_2.fq.gz" 36 36 }}} 37 37 … … 44 44 45 45 {{{ 46 bsub bismark_methylation_extractor -p --gzip --bedGraph trimmedReads_bismark_bt2_pe.bam 46 sbatch --partition=20 --job-name=bme--mem=32G --wrap "bismark_methylation_extractor -p --gzip --bedGraph trimmedReads_bismark_bt2_pe.bam" 47 47 }}} 48 48 * The resulting file, trimmedReads_bismark bt2_pe.bismark.cov.gz, summarizes coverage in the following [https://github.com/FelixKrueger/Bismark/blob/master/Docs/README.md format]:
