Running STAR on multiple replicates

Question

[Pac314]

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?

Answer 1

[swbarnes2]

I think each run's results overwrote the previous results. You have to fix that.

[rpolicastro]

Yea, if you don't provide the argument --outFileNamePrefix it will name everything the same (and thus overwrite previous files).

[Pac314]

Ah silly me! Thank you!