No GeneCount and bam outputs-STAR2.52a

[Aditya Saxena]

Hi STAR community! I am trying to run the following script:

STAR-2.5.2a/source/STAR --runThreadN 24 --genomeDir mus_OrthoSet4_STARIndex --readFilesIn M3FL1_S1_L004_R1_001_Trimmed.fastq --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --sjdbGTFfile mus_OrthoSet4_STARIndex/musAnno4_1To1Orthologs.gtf --outFileNamePrefix M3F1_OrthoSet4 

The .out for this job reports 'finished successfully'. I can see 89.48% reads mapped uniquely to the reference in the Log.final.out. 

However, I get an error that reports --outSAMtype: command not found. I also do not see any of the following expected outputs-

ReadsPerGene.out.tab

sortedByCoord.out.bam

toTranscriptome.out.bam

STARgenome (directory)

Shall be very grateful for any advice or help!!

[Alexander Dobin]

Hi Aditya,

--outSAMtype: command not found.

means that you split your command line into two lines, and it only run STAR with --runThreadN 24 --genomeDir mus_OrthoSet4_STARIndex --readFilesIn M3FL1_S1_L004_R1_001_Trimmed.fastq, hence no expected output.

Also, please switch to later STAR release: 2.7.2d or 2.7.3a

Cheers

Alex