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HiS-NET-Seq_pipeline/config_example.yaml
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| # sample ids | |
| sampleID : test | |
| # InputFile: | |
| file: /project/ReadThrough/HiS-NET-Seq_pipeline/data/test/test.fastq.gz | |
| reference: GRCh38.p12 | |
| spikeIn: GRCm38.p6 | |
| prefix: Mus_musculus_ | |
| # compression type, gz or bz2 | |
| compression: gz | |
| barcode_len: 10 | |
| barcode_linker: CTGTAGGCACCATCAAT | |
| # star path | |
| star : /project/owlmayer/Applications/STAR-2.7.3a/bin/Linux_x86_64/STAR | |
| # star index path | |
| star_index : /project/ReadThrough/HiS-NET-Seq_pipeline/data/GRCh38_p12_GRCm38_p6 | |
| star_params: /project/ReadThrough/HiS-NET-Seq_pipeline/data/Parameters.in | |
| annotation: /project/ReadThrough/HiS-NET-Seq_pipeline/data/gencode.v28.vM18.primary_assembly.annotation.gff3 | |
| genome_fa: /project/ReadThrough/HiS-NET-Seq_pipeline/data/GRCh38.p12.GRCm38.p6.primary_assembly.genome.fa | |
| #FastQC | |
| fastqc : /usr/local/package/bin/fastqc | |
| # samtools | |
| samtools : /usr/local/package/bin/samtools | |
| starcode: /project/owlmayer/Applications/starcode/starcode | |
| starcode_params: "-d 0" | |
| cutadapt: /usr/local/package/bin/cutadapt | |
| cutadapt_params: "-a ATCTCGTATGCCGTCTTCTGCTTG -a AAAAAAAAAAGGGGGGGGGGGGGG -a GGGGGGGGGGGGGGGGGGGGGGG -e 0.2 -q 5 --max-n 0.9" | |
| bedGraphToBigWig : /usr/local/package/bin/bedGraphToBigWig | |
| mask_bed: /project/ReadThrough/HiS-NET-Seq_pipeline/data/masked.bed | |
| star_params_unmapped: /project/ReadThrough/HiS-NET-Seq_pipeline/data/Parameters.unmappedin | |
| stats_bed: /project/ReadThrough/HiS-NET-Seq_pipeline/data/maskingClasses.bed | |
| mask_downstream: 300 |