Hi , I want detect some genes expression using my RNAseq data .My RNAseq data from a mixed strains sample.there are two species in the sample.The gene that I want to detect is homologous in the two species.I did the blast for the two genes and found they are 86% Identities.My expectation is that one gene can not express and the other gene express very highly.But I think the reads from two genes are very similary and they can map the same position and I don't know how to do it. My question is that :How can I determine which gene is expressing using RNAseq data?Can you recommend some software to do this ? Thank you .
Are there small differences between the two copies (e.g. SNP's)? That may help you decide if one or both copies are being expressed. Unless you had UMI's (or ideally full length long read sequencing) precise origin of reads is going to be difficult to establish.
Thank you for your reply.I blast the two genes and they are some SNPs and indels.But I dont know the fact sequence of my RNAseq and dont konw what is the next step.
Just to clarify, did you already ttry o simply align your fastq files to the reference and then use a GTF file to get counts, e.g. with featureCounts? Maybe they are similar but on a sequence level "unique enough" so that good'old alignment can distunguish them.
OK.I will try .thank you .