Hello. When I modify the complexIndels setting to be TRUE -- as opposed to the default setting of false -- I have a shorter runtime and actually find slightly fewer indels. I am confused by this; I would have thought setting this to TRUE would result in longer times and more indels. I started looking into this, after a similar finding that setting indel length to 1 (indels=1 instead of default of 5) dramatically reduced run time. Can you help me understand these settings? My purpose in the analysis is differential gene expression based on total RNA-Seq, so indels and variants are not a key factor - but I am trying to ensure I optimize settings for efficiency with large datasets, and to obtain the best mapping results. Thank you in advance for your help!
#CODE WITH COMPLEX INDELS AS TRUE align(index=MyIndex, readfile1=R1, readfile2=R2, type="rna", minFragLength=50, maxFragLength=600, maxMismatches=3, unique=TRUE, nthreads=7, output_format="BAM", indels=1, TH1=3, TH2=1, complexIndels=TRUE); #Results as follows: #Total_fragments 81428563 #Mapped_fragments 73728794 #Uniquely_mapped_fragments 73728794 #Multi_mapping_fragments 0 #Unmapped_fragments 7699769 #Properly_paired_fragments 69079933 #Singleton_fragments 743665 #More_than_one_chr_fragments 78673 #Unexpected_strandness_fragments 7749 #Unexpected_template_length 2547646 #Inversed_mapping 1271128 #Indels 543377 #Running time : 59.5 minutes #CODE WITH DEFAULT, SO COMPLEX INDELS IS FALSE align(index=MyIndex, readfile1=R1, readfile2=R2, type="rna", minFragLength=50, maxFragLength=600, maxMismatches=3, unique=TRUE, nthreads=7, output_format="BAM", indels=1, TH1=3, TH2=1); #Results as follows: #Total_fragments 81428563 #Mapped_fragments 73725382 #Uniquely_mapped_fragments 73725382 #Multi_mapping_fragments 0 #Unmapped_fragments 7703181 #Properly_paired_fragments 69067023 #Singleton_fragments 703253 #More_than_one_chr_fragments 77453 #Unexpected_strandness_fragments 8606 #Unexpected_template_length 2543287 #Inversed_mapping 1325760 #Indels 544768 #Running time : 99.1 minutes sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.3 (Ootpa) Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  Rsubread_2.4.2 loaded via a namespace (and not attached):  compiler_4.0.3 Matrix_1.3-2 grid_4.0.3 lattice_0.20-41