Hi everyone,
I am trying to generate genome indexes with STAR to align my RNAseq data,
with this command line:
/data/software/STAR/source/STAR --runThreadN 16 --runMode genomeGenerate --genomeDir star_genome3/ --genomeFastaFiles Pvulgaris_442_v2.0.fa --sjdbGTFfile phavu.G19833.gnm2.ann1.PB8d.gene_exons.gff3 --sjdbGTFfeatureExon exon --sjdbGTFtagExonParentTranscript Parent --genomeChrBinNbits 18 --sjdbOverhang 100
but after 5 min it ends, I think that have problem with such speedy.
The list output of it is here:
Genome SAindex chrName.txt chrStart.txt exonInfo.tab genomeParameters.txt sjdbList.fromGTF.out.tab transcriptInfo.tab SA chrLength.txt chrNameLength.txt exonGeTrInfo.tab geneInfo.tab sjdbInfo.txt sjdbList.out.tab
Then I change runmod to alignment with this script:
/data/software/STAR/source/STAR --runMode alignReads --genomeDir /data/mshoorooei/star_genome4/ --runThreadN 16 --outFilterMismatchNmax 2 --readFilesIn PE_27_F.fq.gz PE_27_R.fq.gz --readFilesCommand gunzip -c --outFileNamePrefix 27_ --outReadsUnmapped unmapped_27 --outSAMtype BAM SortedByCoordinate
Output is here:
27_Aligned.sortedByCoord.out.bam
27_Log.final.out
27_Log.out
27_Log.progress.out
27_SJ.out.tab
unfortunately, this gives me the same problem too.
Do you have any idea? thanks for your suggestions.