GSE279064 eCLIP Data Processing

eCLIP geo_data_processing 3 steps

Publication

LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.

bioRxiv : the preprint server for biology (2025) — PMID 39868246

Dataset

GSE279064

LARP6 shapes the mRNA translation of fibrogenic genes [RNA-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

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  1. 1

    for ribosome profiling, reads were processed with CTGTAGGCACCATCAAT adapter trimming using cutadapt.

    cutadapt
  2. 2

    Bowtie1 alignment was used for hg38 rrna and trna.

    Bowtie
  3. 3

    Unaligned reads from previous step were aligned to genomic hg38 , followed to trasncriptomic hg38.

Raw Source Text 
for ribosome profiling, reads were processed with CTGTAGGCACCATCAAT adapter trimming using cutadapt.
Bowtie1 alignment was used for hg38 rrna and trna.
Unaligned reads from previous step were aligned to genomic hg38 , followed to trasncriptomic hg38.
Assembly: GRCh38
Supplementary files format and content: wiggle files of 5' aligned rna-seq and ribosome profiling p-site. Each file is separated for plus and minus strand.
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