Links used across pipelines

The use of hard links is to make sure that common tasks shared across different pipelines are consistent and to reduce the risk of errors. The following hard links are used across the pipelines:

Suppose . is the root of the project directory.

• FastQC processing of pre-trimmed reads:

  • transcriptome -> chromatin_accessibility

  ln ./transcriptome/pre-alignment_processing/fastqc_pre-trimming.sh \
    ./chromatin_accessibility/pre-alignment_processing/fastqc_pre-trimming.sh
  

  • transcriptome -> protein_dna_interaction

  ln ./transcriptome/pre-alignment_processing/fastqc_pre-trimming.sh \
    ./protein_dna_interaction/pre-alignment_processing/fastqc_pre-trimming.sh
  

• Trimming of reads with fastp

  • chromatin_accessibility -> protein_dna_interaction

  ln ./chromatin_accessibility/pre-alignment_processing/trimming_reads.sh \
    ./protein_dna_interaction/pre-alignment_processing/trimming_reads.sh
  

• FastQC processing of post-trimmed reads:

  • chromatin_accessibility -> protein_dna_interaction

  ln ./chromatin_accessibility/pre-alignment_processing/fastqc_post-trimming.sh \
    ./protein_dna_interaction/pre-alignment_processing/fastqc_post-trimming.sh
  

• Alignment with Bowtie2

  • transcriptome -> chromatin_accessibility

  ln ./chromatin_accessibility/alignment/bowtie2_align.sh \
    ./protein_dna_interaction/alignment/bowtie2_align.sh
  

• Deduplication of aligned reads

  • chromatin_accessibility -> protein_dna_interaction

  ln ./chromatin_accessibility/post-alignment_processing/dedup_bam.sh \
    ./protein_dna_interaction/post-alignment_processing/dedup_bam.sh
  

• Filtering and indexing of aligned reads

  • chromatin_accessibility -> protein_dna_interaction

  ln ./chromatin_accessibility/post-alignment_processing/filter_index_reads.sh \
    ./protein_dna_interaction/post-alignment_processing/filter_index_reads.sh
  

• Fragment size distribution

  • chromatin_accessibility -> protein_dna_interaction

  ln ./chromatin_accessibility/post-alignment_processing/fragment_size.sh \
    ./protein_dna_interaction/post-alignment_processing/fragment_size.sh