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How can I retrieve TPM values for selected genes from transcriptome data in a Bioproject on NCBI?

https://www.ncbi.nlm.nih.gov/bioproject?LinkName=biosample_bioproject&from_uid=4262220

The Bioproject I am interested in is the above, containing transcriptome data from different tissues in Rousettus aegypticus. There are 21 biosamples in this collection (each containing data from a different tissue).

Can someone please tell me the process to retrieve the gene expression levels in each individual tissue (biosample)?

I am new to bioinformatics, and would appreciate any help!

Thanks. A

rna-seq assembly genome next-gen
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written by A248 • A248

1 answer

SRA generally has raw sequence data. You will need to download and align the data yourself to the transcriptome (assuming they have made it available or you will need to use something like trinity to assemble it yourself) to get the counts (or any other derived measure downstream). You can find all sample fastq files at EBI-ENA here. Use the bulk download to get them all.

Edit: Looks like they have submitted the assembled transcriptome here. Download the fasta file.
Edit 2: Using salmon would be a fast way of getting the counts.

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written by GenoMax GenoMax

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