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Running STAR on multiple replicates

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?

rna-seq
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updated by swbarnes2 swbarnes2 • written by Pac314 • Pac314

1 answer

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

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written by swbarnes2 swbarnes2

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

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written by rpolicastro rpolicastro

Ah silly me! Thank you!

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written by Pac314 • Pac314

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