Hello Bioc, I am running some tests to compare trimLRpatterns vs other trimming tools (skewer, cutadapt, AdapterRemoval).
I have generated simulated data using ART (https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm). In particular, there is a modified version of the program from the authors of Skewer that allows to simulate the contamination with adaptors (http://sourceforge.net/projects/skewer/files/Simulator/). For my simulations, I have created reads of 150 bp for a coverage of 20x, and a fragment size of 200 bp +- 50 bp, to simulate the contamination with adaptors in those reads with small fragment size. The quality profiles were taken from actual MiSeq E. coli Fastq files. Most of the programs achieve a sensibility/specificity of 99%. trimLRpatterns is showing high specificity (99%) but a very low sensibility (max. 16%), having problems to remove the adaptors globally. I have changed different parameters, but I can't improve the value. Attached is a test script for a portion of the simulated data, where I'm varying max.Rmismatch from 1 to 50. I know exactly the length of the true trimmed reads, the location in the genome is attached in the bed file. So, the width can be compared with the output of the program. I am using the same statistics of the AdapterRemoval paper. Any advice in relation to this? Thanks! Leandro
"seqnames" "start" "end" "width" "strand" "score" "id" "1" "CP014314.1" 5062689 5062838 150 "+" 500 "CP014314.1-730480/1-1" "2" "CP014314.1" 1075192 1075341 150 "+" 500 "CP014314.1-730478/1-1" "3" "CP014314.1" 3863918 3864067 150 "-" 500 "CP014314.1-730476/1-1" "4" "CP014314.1" 13223 13372 150 "+" 500 "CP014314.1-730474/1-1" "5" "CP014314.1" 1849614 1849763 150 "-" 500 "CP014314.1-730472/1-1" "6" "CP014314.1" 3241900 3242049 150 "+" 500 "CP014314.1-730470/1-1" "7" "CP014314.1" 1024887 1025036 150 "-" 500 "CP014314.1-730468/1-1" "8" "CP014314.1" 4175330 4175479 150 "-" 500 "CP014314.1-730466/1-1" "9" "CP014314.1" 754001 754150 150 "-" 500 "CP014314.1-730464/1-1" "10" "CP014314.1" 3243909 3244058 150 "+" 500 "CP014314.1-730462/1-1" "11" "CP014314.1" 1497355 1497504 150 "+" 500 "CP014314.1-730460/1-1" "12" "CP014314.1" 2578074 2578223 150 "-" 500 "CP014314.1-730458/1-1" "13" "CP014314.1" 4709715 4709864 150 "-" 500 "CP014314.1-730456/1-1" "14" "CP014314.1" 2261143 2261292 150 "-" 500 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