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?
Well, how different? Are most of the gene counts within 5% of each other?
more than 10 times much
Request the manuscript authors for scripts used in analysis explaining why you would need those scripts. Authors will be happy to furnish. If not, contact publishers. Authors are supposed to furnish the scripts used in analysis.