Hi I wrote this small script in order to be able to analyze read from CHIP
seq data. This script allow me to get from one read sequence all the
possible combination by removing a base at each side of the read until no
base are left. my issue is that I dont find the way to pull all the output
into one csv or xls file with the name of the sample (read name) and the
full list of combination.script#j=1#nr<-nrow(seq2)#n=1#while (n<nr) {
#p<-str_length(seq2[n,2]) #i<-1:p #while (j<=p) {
seqpart<-(str_sub(seq2[n,2], start=i[i], end=-j))#print(seq2[n,1])#out.files
<-seqpart#write.csv(seqpart, out.files[n])#j=j+1#}#j=1#n=n+1#print(n)#}I am
sure that we have better ways to do that, but I am just a beginner in
R.....My input are a excel spread shit name seq1.s Col31 AA1
CAAGGCGCGCGT
AE2 AB1 GGTACACAATATATGGTGTGCGTGCGTGCG AF mod3 AC1
AGTGCGTGAAAACCGTC AI4 AD1
AAAGTGTGTGCCACAC AG5 AE1 TGACTGACT AB6 AF1
TAGTTGCAACGTTGCAGCGTTGCA AH full7
AG1 AACGCGCCGTTAACGTTGACACGTGTGT AD mod8 AH1
ACGTGGAGTGCGTGTGTACACGTGTG Ai
full9 AI1 TGAACAGTGGTACGTACATGCGTACGTTAACG AC longer10 AJ1
CATGCATGCATGCATGCAT AAand the ouput I can get for the first sequence is for
one run
"","x""1","CAAGGCGCGCGT""2","AAGGCGCGCGT""3","AGGCGCGCGT""4","GGCGCGCGT""5","GCGCGCGT""6","CGCGCGT""7","GCGCGT""8","CGCGT""9","GCGT""10","CGT""11","GT""12","T"with
this script I am getting a number of file according to p. I would like to
merge all the file from one sequence to one first, remove all duplicate like
"" and then merge all the file together with gene or read name and full list
of possible combination in order to extract from all the possible
combination repeat pattern.Thanks a lotPAPY
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