How to search the expression of a gene in a transcriptome
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10 months ago
Monocyte • 0

Hello,

I do not understand a lot of things in bioinformatics, so the answer to my question is probably over there, sorry if I did not realize it.

I want to know if some genes are expressed in an organ, and I already have some transcriptome SRA numbers but I do not know how to do the searching. I have read about the SRA toolkit but I do not know to program, and about the SRA database in BLAST. So my questions are

1) ¿Is there another way to search if a gene is represented in the given transcriptome other than SRA toolkit? 2) I understand that SRA contains the reads given by the sequencer. So If I do a BLAST with the SRA database a. What should I introduce the gene or the RNA? b. Will it give only reads (nothing annotated, any protein name)? c. If yes, how can I say those reads are from some specific gene?
3) References?

Thank you very much for your time, Mónica.

RNA-Seq Transcriptomics SRA BLAST • 251 views
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The SRA is a collection of raw sequencing data so unless you know how to process them they will not be useful for you, and the processing is nothing that you simply learn overnight.

Instead you should look for an interactive browser such as the GTEx portal https://www.gtexportal.org/home/ which you can use to explore gene expression in different tissues. Alternatively check studies which have done RNA-seq in organs and see if the supplement contains expression tables.

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Thank You for the link.

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Please do not add answers unless you're answering the top level post. Use the Add Comment/Add Reply options appropriately instead.

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