gravatar for niranjanpandeshwar

2 hours ago by

I am trying to run STAR aligner for arabidopsis thaliana. I am using the commands as mentioned below. I am doing this to compare my results with that obtained from TOPHAT mapper. I am using default parameters in tophat. The mapping percentage is much higher in STAR compared to TOPHAT. Is there any parameter I need to set specifically to match with TOPHAT? Also is there anything specific I need to set for Arabidopsis Thaliana?

% of uniquely matches is higher in STAR(34%) compared to TOPHAT(26%). Overall mapping - STAR (97%), TOPHAT(76%).

Reference files have been taken from ENSEMBL website

Thanks in advance.

STAR genome build command:

STAR --runThreadN 16 --runMode genomeGenerate --genomeDir /home5/STARgenome --genomeSAindexNbases 10 --genomeFastaFiles /home5/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --sjdbGTFfile /home5/Arabidopsis_thaliana.TAIR10.46.gtf --sjdbOverhang 100

STAR command to align reads:

STAR --genomeDir home5/STARgenome --runThreadN 16 --readFilesIn <(gunzip -c fastq.gz) --genomeLoad LoadAndKeep --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 2 --limitBAMsortRAM 50000000000 --outFileNamePrefix home5/star/sample1 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard



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