Hi all! I have some RNA-seq (single-read) datasets divided in two different SRA, one with ~30 million reads and the other with ~15 million reads. I have been reading that I could merge the fastq files, sam or bam files and I would like to know if there is any differences regarding the quality of the final dataset. Thanks!!
There should not be as long as you process them identically before merging the BAM files.