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GEO search filtering

Hello everyone! I am a beginner to this platform and bioinformatics at all. I would like to practise in RNA-seq more. I used a public data for my first analysis. And I would like to do analyzes in another data, too. I would like to use GEO to find another dataset. How can I use filters effectively to search? I am interested in hg19 built, rna-seq data and the dataset they used tophat2-subread(featureCounts) duo.

Thank you for your helps..

geo rnaseq filter
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updated by btsui btsui • written by cilgaiscan • cilgaiscan

I am not sure what this final sentence means.

I am interested in hg19 built, rna-seq data and the dataset they used tophat2-subread(featureCounts) duo.

You can find any human data by searching GEO (I would suggest using EBI-ENA to get fastq files directly). You could choose to align the data against hg19 or GRCh38 (current build). Any aligner (avoid TopHat if you can) followed by counting with featureCounts. If you use STAR you can do the counting on the fly during alignments with an additional option.

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written by GenoMax GenoMax

1 answer

Use google: "RNA-seq" "hg19" site:https://www.ncbi.nlm.nih.gov/geo/

This query will return all the pages in GEO with RNA-seq and hg19 detected.

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written by btsui btsui

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