I need to increase my sequencing depth, so will be generating more reads that will first be trimmed (Trimmomatic) before aligning with STAR. Is there a simply way to just trim and align only the new reads and merge this output with the old STAR output, or do I have to re-run STAR again using all read files (both old and new)? I figure there must be a way to do this, but if it was in the manual I missed it.
For reference, the command I am using in STAR is below. Thanks in advance for any help with this.
STAR --runThreadN 10 --genomeDir path_to_genomeDir/ \
--readFilesIn path_to_R1_paired_trimmed.fq.gz path_to_R2_paired_trimmed.fq.gz \
--readFilesCommand zcat --outReadsUnmapped Fastx
Thank you! Quite an easy solution