Hello everybody I'm running snpcalling on RNASeq data. My data are related to 6 sample including two conditions, control and treatment with 3 replicates for each. I want to use the star aligner. I am confused at alignment step. Do I need to align three replicate of each condition with genome reference in one run and create one BAM file for each condition? then, I assign reads of each BAM file (3 replicate of control or treatment) to a specific read group with AddOrReplaceReadGroups (picardtools). So, I will achieve one vcf file for each condition and then I have to compare them.
DO i need to align each replicate (Including 2 fastq file) with my reference genome and create a BAM file for each replicate. then, should I assign reads of each BAM files (each replicate) to a specific reads group with AddOrReplaceReadGroups. next step, should I merge vcf files related to the replicate of each condition. Eventually I get two vcf files, each of which is the result of merging the vcfs of replicates.