i used a stupid way to do statistics on the reads distribution varied with N
number
library(ShortRead)
reads <- readFastq(fastqfile);
ids<- id(reads);
seqs <- sread(reads);
# do you know how to get such information by a bioconductor function
nCount<-alphabetFrequency(seqs)[,"N"]
nCountHist<-hist(nCount,breaks=max(nCount))
nCountHist["breaks"]
nCountHist["counts"]
$breaks
[1] 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
24
[26] 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
49
[51] 50 51 52 53 54 55
> nCountHist["counts"]
$counts
[1] 16988332 3975 4365 3099 2760 2473 2918 3045
[9] 3320 3028 3290 3560 4695 4546 3939 4255
[17] 3899 4025 6764 3554 4056 2716 1812 1456
[25] 1618 2133 2253 1809 1638 924 951 889
[33] 931 1089 1868 3344 348 36 20 25
[41] 12 16 10 24 9 4 4 3
[49] 0 0 3 1 1 0 1
what i need is just the count of reads varied with "N" number, like such
above
thx
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