Finding gene of interest in data downloaded from SRA

Question

[bdoescience]

Hey All,

I am new in the bioinformatics world as a biologist. So things are quite different and complicated. If my questions are silly, please forgive me.

I downloaded some data sets of different species of a bacteria from SRA, and converted them to FASTQ format. However, I am not sure about the next step. I am planning to have a look at whether my gene of interest were expressed in the data sets. I just want to see whether my gene were presence or absence in it. What is the easiest/simplest way to do it?

Thank you for you helps.

Stay home, stay safe!

Regards

B

[GenoMax]

I am planning to have a look at whether my gene of interest were expressed in the data sets.

Be sure to only select RNAseq datasets from SRA. Otherwise you would just know if the gene was present in genome or not. Not if it was expressed.

You can align these datasets to the gene sequence of your choice using it as a reference. It is not the ideal thing to do but if you are looking for a qualitative answer then this will suffice.

Answer 1

[swbarnes2]

If you have fastqs, there is no good simple way (unless you want to try and just grep for a snippet of your gene) ; you are going to have to align and do gene counting. So you'll need a reference fasta and a gtf or gff to know where the genes are on the genome.

[bdoescience]

Thank you for answer. I have reference fasta and gff. At this point, the main issue is tools. Since there are lots of different tools, I'm struggling with choosing which one is the best for me.

Answer 2

[vkkodali_ncbi]

If you have SRA identifiers you can use BLAST and choose SRA as the database as shown in the image below. Note, there is a limit on the size so while you may be able to enter multiple SRA identifers you won't be able to search for your favorite gene across the entire SRA.