Hi, guys.
I'm processing some smRNA-seq data which are single-end data with STAR. (ENCODE PIPELINE guide line)
But when I do QC with qualimap2 after the alignment, some samples get strange value or no values at the transcript coverage profile lines. (ex. absence or some weird value like 477)
Does someone have experience in this kind of error? Why does this happen in some samples and some don't...I can't figure it out....
My STAR mapping options were like this,
--genomeDir $STARgenomeDir --readFilesIn $read1 --outSAMunmapped None \ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts \ --outFilterMultimapNmax 20 --clip3pAdapterMMp 0.1 --outFilterMismatchNoverLmax 0.03 \ --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1
And my qualimap command line was like this,
qualimap rnaseq --algorithm uniquely-mapped-reads -bam output/hg19/Aligned.sortedByCoord.out.bam -gtf /gencode.v19.annotation.gtf -oc countsQC -outformat HTML --sequencing-protocol non-strand-specific --java-mem-size=10G -outdir hg19
Thank you very much
