spikeIn sampe scaling factor calculation discrepenses

[sunta3iouxos]

I am getting different results using the multiBamSummary command on my local PC using the following command that I expected to be the same on the server side, and I am suspecting that this is probably the issue: my command:

multiBamSummary bins --binSize 10000 --blackListFileName /home/tgeorgom/CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikesTEST/annotation/blacklist.bed --ignoreDuplicates -p 8 --bamfiles /mnt/c/AP04/split_bam/*host*bam  -out /mnt/c/AP04/mergedBam/deeptools/multiBAM_SPIKE_bin1000.out.npz --scalingFactors /mnt/c/AP04/mergedBam/deeptools/multiBAM_spike_scaling_q2.txt  --minMappingQuality 2

Number of bins found: 273590 the output:

sample	scalingFactor
A006850324_209957_S1_L000_spikein.bam	1.0099
A006850324_209960_S2_L000_spikein.bam	1.1728
A006850324_209962_S3_L000_spikein.bam	0.8376
A006850324_209964_S4_L000_spikein.bam	1.0653
A006850324_209966_S5_L000_spikein.bam	0.8244
A006850324_209968_S6_L000_spikein.bam	0.9989
A006850324_209970_S7_L000_spikein.bam	1.0220
A006850324_209972_S8_L000_spikein.bam	1.0535
A006850324_209974_S9_L000_spikein.bam	1.1026
A006850324_209976_S10_L000_spikein.bam	1.0160
A006850324_209978_S11_L000_spikein.bam	1.0301
A006850324_209980_S12_L000_spikein.bam	1.0347
A006850324_209982_S13_L000_spikein.bam	1.0306
A006850324_209984_S14_L000_spikein.bam	0.9753
A006850324_209986_S15_L000_spikein.bam	0.9549
A006850324_209988_S16_L000_spikein.bam	0.9313
A006850324_209990_S17_L000_spikein.bam	0.8619
A006850324_209992_S18_L000_spikein.bam	1.0217

and this is what I am using on the server side:

ChIP-seq -d /scratch/tgeorgom/AP04/ --useSpikeInForNorm --getSizeFactorsFrom genome --sampleSheet /scratch/tgeorgom/AP04/pSer5POLII.tsv --windowSize 500 --plotFormat pdf mm10_gencodeM19_spikesTEST /scratch/tgeorgom/AP04/PolII_ChIPtype_all.yalm

Number of bins found: 4687

and the output is as follows:

sample	scalingFactor
A006850324_209957_S1_L000	0.9813
A006850324_209960_S2_L000	1.1281
A006850324_209962_S3_L000	0.8268
A006850324_209964_S4_L000	1.0348
A006850324_209966_S5_L000	0.8089
A006850324_209968_S6_L000	0.9749
A006850324_209970_S7_L000	0.9942
A006850324_209972_S8_L000	1.0490
A006850324_209974_S9_L000	1.0823
A006850324_209976_S10_L000	0.9764
A006850324_209978_S11_L000	0.9942
A006850324_209980_S12_L000	1.0081
A006850324_209982_S13_L000	0.9971
A006850324_209984_S14_L000	0.9630
A006850324_209986_S15_L000	0.9409
A006850324_209988_S16_L000	0.9228
A006850324_209990_S17_L000	0.8261
A006850324_209992_S18_L000	1.0030

Using a different --binSize to recapitulate the Number of bins found, did not solved the issue:

multiBamSummary bins --binSize 500000 --ignoreDuplicates -p 8 --bamfiles /mnt/c/AP04/split_bam/*spikein*bam -out /mnt/c/AP04/mergedBam/deeptools/multiBAM_SPIKE_bin1000.out.npz --scalingFactors /mnt/c/AP04/mergedBam/deeptools/multiBAM_spike_scaling_q2Noblack_bin500000.txt  --minMappingQuality 2

Number of bins found: 5518

sample	scalingFactor
A006850324_209957_S1_L000_spikein.bam	1.0093
A006850324_209960_S2_L000_spikein.bam	1.1931
A006850324_209962_S3_L000_spikein.bam	0.8369
A006850324_209964_S4_L000_spikein.bam	1.0730
A006850324_209966_S5_L000_spikein.bam	0.8210
A006850324_209968_S6_L000_spikein.bam	1.0097
A006850324_209970_S7_L000_spikein.bam	1.0212
A006850324_209972_S8_L000_spikein.bam	1.0618
A006850324_209974_S9_L000_spikein.bam	1.1137
A006850324_209976_S10_L000_spikein.bam	1.0174
A006850324_209978_S11_L000_spikein.bam	1.0432
A006850324_209980_S12_L000_spikein.bam	1.0476
A006850324_209982_S13_L000_spikein.bam	1.0343
A006850324_209984_S14_L000_spikein.bam	0.9812
A006850324_209986_S15_L000_spikein.bam	0.9624
A006850324_209988_S16_L000_spikein.bam	0.9431
A006850324_209990_S17_L000_spikein.bam	0.8646
A006850324_209992_S18_L000_spikein.bam	1.0306