mapped percentage difference of Mageck count (24%)and Mageck-vispr(70%)

[Qingcai Meng]

Hi,

May I ask the mapped percentage difference of Mageck count and Mageck-vispr? When I use this code, I got 24% mapped reads,

mageck count -l mouse_geckov2_library_a_09mar2015-2.csv -n dc2.5 --sample-label "ctrl,GFP" --trim-5 24 --fastq Ctrl_S1_L001_R1_001.fastq GFP_S2_L001_R1_001.fastq

File Label Reads Mapped Percentage TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation NegSelQCPvalPermutationFDR NegSelQCGene
Ctrl_S1_L001_R1_001.fastq ctrl 37233126 9035701 0.2427 22672 388 0.159 0 1 1 1 0.0
GFP_S2_L001_R1_001.fastq GFP 45882461 11286200 0.246 22672 414 0.144 0 1 1 1 0.0

and when I use the Mageck-vispr, I got a 70% mapped reads, but these two analyses were base on exactly the same seq data and library

snakemake --cores 8
vispr server results/*.vispr.yaml

File Label Reads Mapped Percentage TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation NegSelQCPvalPermutationFDR NegSelQCGene
Ctrl_S1_L001_R1_001.fastq ctrl 37233126 25932467 0.6965 65959 1183 0.1596 0 1 1 1 0.0
GFP_S2_L001_R1_001.fastq GFP 45882461 31998924 0.6974 65959 1231 0.1457 0 1 1 1 0.0

Thanks super much,

Qingcai.