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Don't know how to analysis the downloaded data from ENCODE project, including tsv file about gene quantification and transcript quantification
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2.2 years ago

Recently, I downloaded some rna-seq data about hESC and want to find out the specific gene expressed in hESCs rather than other cell type(Also download rna-seq data about fibroblast.). Both data file types are tsv. I am really fresh to data analysis, so forgive me for such boring questions maybe.

RNA-Seq • 1.1k views
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I think it is better to give some data in the TSV file so that we can understand what type of data is in the TSV file. Depend on the TSV data, maybe we can give some hint how to process the data.

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the tsv data mainly including following parts: gene_id, transcript_id, length, effective length, expected_count, TPM, FPKM and several others. I think it is like the data had already been processed and need visualization or what.

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I see. So, you can directly use the data for expression analysis. For example, you can use the expected count as input for DESeq2. Useful keyword for studying is differential expression analysis.

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Got it. Really appreciate it.

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