I have 2 samples with 3 replicates each having PE reads. If I run:
STAR --genomeDir genomeDir/
--readFilesIn Sample1-rep1-read1,sample1-rep2-read1,sample1-rep3-read1, sample1-rep1-read2,sample1-rep2-read2,sample1-rep3-read2
--runThreadN 8
--outSAMtype BAM SortedByCoordinate
--quantMode GeneCounts
STAR --genomeDir genomeDir/
--readFilesIn Sample2-rep1-read1,sample2-rep2-read1,sample2-rep3-read1, Sample2-rep1-read2,sample2-rep2-read2,sample2-rep3-read2
--runThreadN 8
--outSAMtype BAM SortedByCoordinate
--quantMode GeneCounts
I get only this ouput in my ReadsPerGene.out.tab:
N_unmapped 1101143 1101143 1101143
N_multimapping 118148 118148 118148
N_noFeature 780486 2709783 2726521
N_ambiguous 0 0 0
Should I run a single star command on each read pair using a loop instead?