I need some clarifications for the below scenario (RNASeq experiment),
- lane 1 in flowcell contains 4 samples (A, B, C, D) those had been loaded on the lane 2 (A, B) and lane 3 (C, D) as well.
- Before performing downstream analysis, do I need to merge the FASTQ reads from lane 1 with FASTQ reads in lane 2 (similarly for reads from lane 1 with reads in lane 3)?
- Without merging the fastq files, if I do the alignment separately for lane 1, lane 2, and lane 3 with human reference. Does it impact my analysis? then I am planning to merge the two bam files from lane 1 and lane 2 (similarly for lane 1 and lane 3) using sam tools.