Help with data from rna-seq

Question

[lks50]

Hi guys, I have some sugar cane fastq files and I need to find the genes contained in my libraries.

I've already looked at the quality of fastqc sequences, removed the adapters, aligned with HISAT, the generated files were converted to ".bam".

I already used Trinity with the generated ".bam" files and finally got the ".fasta" files from Trinity output.

Now I'm trying to use BRAKER to take notes, but it's been very difficult. So I would like to know if I am on the right track to identify these genes and what possible alternatives for gene identification I have.

Thank you!

[Medhat]

Maybe you should change the question to "Identifying genes from RNA-Seq fastq reads" or something similar to have a more meaningful title.

[h.mon]

You will need to explain in greater detail what you are doing: it is not clear what are your goals, and it seems you are mixing transcriptome and genome assembly and annotations workflows.

aligned with HISAT

Aligned the RNAseq reads to which reference? The sugar cane genome?

I already used Trinity with the generated ".bam" files and finally got the ".fasta" files from Trinity output.

Does this mean you did a reference-guided transcriptome assembly? At any rate, if you used Trinity, the ".fasta" file should contain the assembled transcripts.

Now I'm trying to use BRAKER to take notes

Are you trying to annotate the genome or the transcriptome?

[hafiz.talhamalik]

you should elaborate your question. it's not clear. also as mentioned by @h.mon looks like you are mixing transcriptome and genome analysis

[lks50]

Thanks guys, unfortunately I could not generate the data, I am very confused yet. I started in this area not long ago, I need to read more.

[h.mon]

This tutorial will help you in the "getting help" part of learning:

How To Ask Good Questions On Technical And Scientific Forums