Question: Running STAR on multiple replicates
gravatar for Nish314
14 days ago by
Nish3140 wrote:

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

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 • 90 views
ADD COMMENTlink modified 14 days ago by swbarnes29.2k • written 14 days ago by Nish3140
gravatar for swbarnes2
14 days ago by
United States
swbarnes29.2k wrote:

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

ADD COMMENTlink written 14 days ago by swbarnes29.2k

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

ADD REPLYlink written 14 days ago by rpolicastro2.4k

Ah silly me! Thank you!

ADD REPLYlink written 14 days ago by Nish3140
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