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config.yaml
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prefix: "MEP1"
run_rseqc: False
remove_intermediate_files: False
samples:
- EE_HSC1
- EE_HSC6
- EE_HSC14
- EE_HSC18
- EE_HSC21
- EE_HSC26
- EE_HSC29
directories:
- results/preprocess_01/01_FastQC_raw_data
- results/preprocess_01/02_UMI_extraction
- results/preprocess_01/02_UMI_extraction/Read2s
- results/preprocess_01/03_trimmed_data
- results/preprocess_01/03_trimmed_data/unzipped
- results/preprocess_01/04_FastQC_trimmed_data
- results/preprocess_01/05_sortmernaed_data
- results/preprocess_01/05_sortmernaed_data/zipped
- results/preprocess_01/06_01_FQScreen_trimmed_data
- results/preprocess_01/06_02_FQScreen_sortmernaed_data
- results/preprocess_01/07_star_aligned
- results/preprocess_01/08_umi_deduplicated
- results/preprocess_01/09_01_markdup_beforeumidedup
- results/preprocess_01/09_02_markdup_afterumidedup
- results/preprocess_01/10_featureCounts
- results/preprocess_01/11_TinScore
- results/preprocess_01/12_GeneBodyCov
- logs/01_FastQC_rawdata
- logs/02_UMI_extraction
- logs/03_trimming
- logs/04_FastQC_trimmed
- logs/05_sortmerna
- logs/06_01_FQScreen_trimmed_data
- logs/06_02_FQScreen_sortmernaed_data
- logs/07_staraligner
- logs/08_UMI_deduplication
- logs/09_01_markdup_beforeumidedup
- logs/09_02_markdup_afterumidedup
- logs/10_featureCounts
trimming_params:
quality: 30
length: 30
stringency: 2
sortmerna_ref:
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/silva-euk-28s-id98.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/silva-euk-18s-id95.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/silva-arc-16s-id95.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/silva-arc-23s-id98.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/silva-bac-16s-id90.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/silva-bac-23s-id98.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/rfam-5.8s-database-id98.fasta
- /mnt/groupMansuy/kerem/auxiliary/genome/rRNA_databases/rfam-5s-database-id98.fasta
fastq_screen_conf: "/mnt/IM/groupMansuy/kerem/auxiliary/conf/fastq_screen.conf"
star_genome_dir: "/mnt/groupMansuy/kerem/auxiliary/genome/staridx"
GTF_file: "/mnt/groupMansuy/kerem/auxiliary/genome/GCF_000001635.27_GRCm39_genomic.gtf"
bed_file: "/mnt/groupMansuy/kerem/auxiliary/genome/GRCm39_genomic.bed12"
salmon_index_dir: "/mnt/groupMansuy/kerem/auxiliary/genomes/mm10_salmon_index"
ANALYSIS_DIRS:
- 01_FastQC_raw_data
- 03_trimmed_data
- 04_FastQC_trimmed_data
- 06_01_FQScreen_trimmed_data
- 06_02_FQScreen_sortmernaed_data
- 07_star_aligned
- 09_01_markdup_beforeumidedup
- 09_02_markdup_afterumidedup
- 10_featureCounts
- 12_GeneBodyCov