Problem for downloading Non-coding RNA from Gene Expression Omnibus (GEO)

Hi, I want to download Non-coding RNA profiling by high throughput sequencing from GEO. My favorite data set is GSE114327. In that data set in Supplementary file section, I download just one of the file by clicking on the custom section from GSE114327_RAW.tar. After extracting the file,

I open “GSM3139597_CN34-CM-1_S57_L006_R1_001.hg38.437.oncRNA.cnt.txt” in notepad++ and see below content:

tag_15405   1
tag_29167   1
tag_34351   1
tag_56768   1
tag_68635   1
tag_69423   1
tag_9349    1

And I think this content isn’t the value of Non-coding RNA. I appreciate if anybody helps me to find the right way of downloading that dataset.

non-coding rna geo

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written 7.1 years ago by modarzi

Data processing notes for this set say this:

FASTQ reads were subjected to adapter removal (cutadapt) per manufacturer's instructions (NEXTflex Small RNA Sequencing Kit v3). The degenerate sequences (N4) at the 5 and 3 end of the reads were removed and added to the name of the read as a unique molecular identifier (UMI) using UMI tools. Trimmed reads were mapped to the human genome (build hg38) using Bowtie2 v2.2.8. The resulting bam file was sorted (samtools sort), converted to bed (bamToBed), and intersected with the annotated oncRNAs (intersectBed). The number of reads overlapping each oncRNA were tallied to generate a count file. Genome_build: hg38 Supplementary_files_format_and_content: count file for each feature

You may have to go through their paper to find oncRNA.

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written 7.1 years ago by GenoMax

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