RNA seq alignment

Question

[iamsmor]

Hello everyone

I am newbie on RNAseq alignment. I need to help how will do alignment processes. I have a single end reads data. I am trying to build up stuff that for use hisat2 tools for alignment. I downloaded (shown below).gtf and hg38 snp tran for alignment process

#To download ENSEMBL indexed hg38 human genome and human genome gtf files

#wget --content-disposition:
https://cloud.biohpc.swmed.edu/index.php/s/grch38_snp_tran/download

# gtf file:
wget http://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz 

and first link contained ready index like this "genome_snp_tran.2.ht2 " (I understood this with my lack knowledge). I am not sure how I will continue or I don't know I need fasta for reference or not. I will be very thankful for every little information and help. I am really stuck.

[seidel]

Have you read the manual? It has explanations of the components you need to do an alignment, and how to configure the commands. If you're uncertain and want to build familiarity, you should start with a small sample of your reads, so you can see what the output will look like.