GSE146726 Processing Pipeline

RNA-Seq code_examples 4 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

GSE146726

RNA-Seq of circCDYL knockdown (KD) samples in HepG2, J82, and UMUC3 cells and of GRWD1, IGF2BP1, and IGF2BP2 knockdown (KD) samples in J82 and UMUC3 …

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

    Fastq files demultiplexed using Illumina’s bcl2fastq v2.20.0.422

  2. 2

    Adapters removed using Trim Galore v0.4.1

    Trim Galore v0.4.1
  3. 3

    Reads mapped using TopHat2 and Bowtie2 (version 2.1.1)

    Bowtie2 v2.1.1
  4. 4

    Read counts were estimated using HTSeq (v0.6.1p1)

    HTSeq v0.6.1p

Tools Used

Trim Galore Bowtie2
Raw Source Text 
Fastq files demultiplexed using Illumina’s bcl2fastq v2.20.0.422
Adapters removed using Trim Galore v0.4.1
Reads mapped using TopHat2 and Bowtie2 (version 2.1.1)
Read counts were estimated using HTSeq (v0.6.1p1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized abundance measuments
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