GSE268963 Processing Pipeline
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code_examples
1 step
Publication
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.Molecular cell (2024) — PMID 39303722
Dataset
GSE268963Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [SLAM-Seq]
Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.
Processing Steps
Generate Jupyter Notebook-
1
Reads were aligned to hg38 using SlamDunk (v0.4.3) with inclusion of multi-mapping reads.
$ Bash example
# Install SlamDunk (example using pip) # pip install slamdunk==0.4.3 # Define paths READS_FILE="input_reads.fastq.gz" # Replace with actual input file(s) OUTPUT_DIR="slamdunk_aligned_output" REFERENCE_FASTA="/path/to/hg38.fa" # Placeholder for hg38 reference genome FASTA STAR_INDEX_DIR="/path/to/STAR_index_hg38" # Placeholder for pre-built STAR index for hg38 # Create output directory if it doesn't exist mkdir -p "${OUTPUT_DIR}" # Align reads to hg38 using SlamDunk (v0.4.3) # The --star-args "--outFilterMultimapNmax 100" parameter is used to include multi-mapping reads, # allowing up to 100 alignments per read. Adjust this value if a different threshold is desired. slamdunk align \ -r "${REFERENCE_FASTA}" \ -o "${OUTPUT_DIR}" \ --star-index "${STAR_INDEX_DIR}" \ --star-args "--outFilterMultimapNmax 100" \ "${READS_FILE}"
Raw Source Text
Reads were aligned to hg38 using SlamDunk (v0.4.3) with inclusion of multi-mapping reads. Assembly: hg38 Supplementary files format and content: C->T conversion counts within 3' UTR regions output by SlamDunk