Hi. I'm new in bioinformatics and I'm trying to extract read counts from fastq files.
I used STAR alignment method with GENCODE annotation files.
(I didn't trimmed by reads because I heard that trimming is an option)
Then, I used featurecounts to get my read count matrix.
However, my counts are different from original read count provided by paper researchers.
They used Bowtie2 and TopHat to extract read count.
Now, i'm confused because there seems no standard extraction method for bulk RNAseq.
People use a lot of tools for trimming, alignment, and getting count matrix.
Which data should I trust? or How can I be sure my data is reliable?