I am trying to get no. of reads per gene with STAR --quantMode.
I have followed the
STAR --runMode genomeGenerate --runThreadN 16 --genomeDir /media/rm313/SDC/genomeDir \
--genomeFastaFiles Brassica_napus_v4.1.chromosomes.fa --sjdbGTFfile Brassica_napus.annotation_v5.gtf \
--genomeChrBinNbits 18 --limitGenomeGenerateRAM 910000000000
step to generate Genome.
To get no. of reads, i used
STAR --runThreadN 16 --runMode alignReads --outFilterMultimapNmax 1 \
--outFilterMatchNmin 35 --outSAMtype SAM --quantMode GeneCounts \
--twopassMode Basic --outFileNamePrefix "Wes1" --genomeDir /media/rm313/SDC/genomeDir \
--sjdbGTFfeatureExon /media/rm313/SDC/Brassica_napus.annotation_v5.cds.fa \
--readFilesIn /media/rm313/SDC/W1F.fastq /media/rm313/SDC/W1R.fastq
My questions
1) ReadsperGene.out.tab does not contain No. of reads per gene. it shows
N_unmapped 453074 453074 453074 N_multimapping 258436 258436 258436 N_noFeature 738252 812120 865586 N_ambiguous 0 0 0
2) I need reads per gene. however, it shows on chromosome name in Log.out and SJ.out.tab file.
Can you please suggest, what's wrong with these commands?
Thank you
Your original mapping command had a space between the dashes and the option name (
-- twopassMode Basic
), but I believe your actual command doesn't have this space, otherwise STAR would error out.after you run STAR and you do an
ls -t
command, which files do you see being generated and what's their content?In the second STAR step, it generated Aligned.out.sam, Aligned.out.sam, Log.final.out, Log.progress.out, Log.out, ReadsPerGene.out.tab (already mentioned), SJ.out.tab
What did you mean by that?