GSE145984 Processing Pipeline

RNA-Seq code_examples 5 steps

Publication

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

Genome medicine (2020) — PMID 33287884

Dataset

GSE145984

Total RNA-Seq of KHSRP knockdown (KD) and control samples in HepG2 and K562

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. 1

    Reads were trimmed with Trim Galore v0.4.1 and cutadapt v1.15

    cutadapt v1.15
  2. 2

    Mapping to hg19 was performed with bwa v0.7.17 and samtools v1.9

    samtools v1.9
  3. 3

    We used the CIRI2 pipeline v2.0.6 to detect circRNAs.

  4. 4

    The CIRI2 pipeline was run with a gene transfer format (GTF) file (hg19) to annotate the overlapping gene of the circRNAs

  5. 5

    Expression values of circRNAs were normalized to total reads

Raw Source Text 
Reads were trimmed with Trim Galore v0.4.1 and cutadapt v1.15
Mapping to hg19 was performed with bwa v0.7.17 and samtools v1.9
We used the CIRI2 pipeline v2.0.6 to detect circRNAs. The CIRI2 pipeline was run with a gene transfer format (GTF) file (hg19) to annotate the overlapping gene of the circRNAs
Expression values of circRNAs were normalized to total reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include counts per million (CPM) values for each circRNA in each sample
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