RNAseq STAR mapping with clipping

Question

[asta.tranholm]

Hi,

I'm writing as I have obtained an RNAseq dataset and have commenced mapping with STAR. I have chosen to add the option of clipping the reads using the added option: '--clip3pNbases 75', to clip 75 bases from the end of the read. I am working with an RNAseq dataset where reads are 150bp. I have used the following code:

STAR --genomeDir  ~/RNAseq/Resources/STAR_idx/ \
         --runThreadN 6 \
         --readFilesCommand zcat \
         --readFilesIn ~/RNAseq/DRG_genewiz2/00_fastq/${x}_R1_001.fastq.gz ~/RNAseq/DRG_genewiz2/00_fastq/$$
         --outFileNamePrefix ~/RNAseq/DRG_genewiz2/STAR_output_genewiz2/${x} \
         --outTmpDir ~/RNAseq/temp \
         --outSAMtype BAM SortedByCoordinate \
         --quantMode GeneCounts \
         --clip5pNbases 0 \
         --clip3pNbases 75
done

However when I open the Log.final.out file for my mapping it lists average mapped length as ~149. To me this sounds like the clipping hasn't occurred? Perhaps I am misunderstanding something? I hope someone can clarify.

[GenoMax]

Have you looked at the resulting BAM files to see if the alignments only show 75 bp?

Answer 1

[asta.tranholm]

I realized that the average mapped length of ~149 corresponds to the clipping having occurred. Had the reads not been clipped, the average mapped length would have been 300 when sequencing is carried out with 150bp reads.