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Is there a bug in the HOMER 4.7 function makeTagDirectory?
I have 2 samples, input and IP.
Here are the statistics calculated by HOMER's makeTagDirectory in the fil tagCountDistribution.txt.
The input sample has 0 tags at over 96% of the positions.
The IP samples has 0 tags at less than 20% of the positions.
Yet, as one would expect, the coverage of the input sample is much better than the coverage of the IP sample when one looks at the coverage in IGV.
For the IP sample, the results make sense, and confirm that there was either too little starting DNA or too many PCR rounds.
For the input sample however, I would intuitively expect the number of positions with 0 tags to be much lower than for the IP sample.
I am using homer v4.7.
I have 2 samples, input and IP.
Here are the statistics calculated by HOMER's makeTagDirectory in the fil tagCountDistribution.txt.
The input sample has 0 tags at over 96% of the positions.
The IP samples has 0 tags at less than 20% of the positions.
Yet, as one would expect, the coverage of the input sample is much better than the coverage of the IP sample when one looks at the coverage in IGV.
For the IP sample, the results make sense, and confirm that there was either too little starting DNA or too many PCR rounds.
For the input sample however, I would intuitively expect the number of positions with 0 tags to be much lower than for the IP sample.
I am using homer v4.7.
Code:
[blancha@lg-1r17-n03 Input_FLe12_5]$ more tagInfo.txt name Unique Positions Total Tags genome=mm10 170193782 91440184.0 fragmentLengthEstimate=168 peakSizeEstimate=257 tagsPerBP=0.033587 averageTagsPerPosition=0.067 averageTagLength=49.711 gsizeEstimate=2722470816 averageFragmentGCcontent=0.413 chr1 13104494 6993040.5 chr2 12334970 7066286.5 chr3 10720381 5721401.5 chr4 10207012 5445184.0 chr5 10006831 5335813.5 chr6 9969654 5339452.5 chr7 8926140 4758013.5 chr8 8569133 4569038.0 chr9 8502297 4587398.5 chr10 8835451 4713878.5 chr11 8452667 4536809.0 chr12 7684680 4102913.0 chr13 7921326 4227154.0 chr14 7658104 4111375.5 chr15 6938730 3706428.5 chr16 6640894 3544058.5 chr17 6185700 3310313.0 chr18 6156391 3285813.5 chr19 4072469 2171806.0 chrX 7176341 3811942.5 chrY 106510 57726.5 chrM 23607 44337.0 cmd=makeTagDirectory /sb/project/afb-431/BIF/KMI/KMI-BIF-P5/results/homer_makeTagDirectory/Input_FLe12_5 /sb/project/afb-431/BIF/KMI/KMI-BIF-P5/results/bowtie/Input_FLe12_5/Input_FLe12_5_sorted_by_coordinates.bam -illuminaPE -checkGC -genome mm10
Code:
[blancha@lg-1r17-n03 Input_FLe12_5]$ more tagCountDistribution.txt Tags per tag position (Median = 0, tags per genomic bp = 0.034) Fraction of Positions 0 0.936717 1 0.062857 2 0.000308 3 0.000046 4 0.000019 5 0.000009 6 0.000005 7 0.000004
Code:
[blancha@lg-1r17-n03 IP_RiPA_FLe12_5]$ more tagInfo.txt name Unique Positions Total Tags genome=mm10 44549627 90536098.5 fragmentLengthEstimate=157 peakSizeEstimate=257 tagsPerBP=0.033255 averageTagsPerPosition=1.749 averageTagLength=49.715 gsizeEstimate=2722466970 averageFragmentGCcontent=0.445 chr1 3292475 6687509.5 chr2 3340909 6979370.5 chr3 2561532 5239035.5 chr4 2755588 5533429.0 chr5 2766469 5552822.5 chr6 2516654 5127843.5 chr7 2540786 5083252.0 chr8 2288444 4608478.5 chr9 2292052 4641111.5 chr10 2212607 4479389.0 chr11 2483818 4969326.5 chr12 1977278 4002612.5 chr13 2032634 4125123.0 chr14 1914642 3892123.0 chr15 1845721 3721216.5 chr16 1611829 3292242.0 chr17 1713574 3688689.0 chr18 1530866 3108415.0 chr19 1158212 2325770.5 chrX 1680513 3425910.0 chrY 31550 49108.0 chrM 1474 3321.0 cmd=makeTagDirectory /sb/project/afb-431/BIF/KMI/KMI-BIF-P5/results/homer_makeTagDirectory/IP_RiPA_FLe12_5 /sb/project/afb-431/BIF/KMI/KMI-BIF-P5/results/bowtie/IP_RiPA_FLe12_5/IP_RiPA_FLe12_5_sorted_by_coordinates.bam -illuminaPE -checkGC -genome mm10
Code:
[blancha@lg-1r17-n03 IP_RiPA_FLe12_5]$ more tagCountDistribution.txt Tags per tag position (Median = 2, tags per genomic bp = 0.033) Fraction of Positions 0 0.198478 1 0.297741 2 0.249510 3 0.141263 4 0.068791 5 0.029349 6 0.010366 7 0.003023