Entering edit mode
4.0 years ago
alhafidzhamdan
•
0
I am looking for help to compute the nucleotide context of the human genome hg38, per region along the chromosomes. Preferably something like this.
GRanges object with 309581 ranges and 98 metadata columns:
seqnames ranges strand | AAA AAC AAG AAT ACA ACC ACG ACT
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
[1] 1 1-10000 + | 0 0 0 0 0 0 0 0
[2] 1 10001-20000 + | 0.0104 0.015 0.0152 0.0056 0.0138 0.0224 0.0044 0.0106
[3] 1 20001-30000 + | 0.0235 0.0127 0.0186 0.0154 0.0193 0.0155 0.0054 0.0147
[4] 1 30001-40000 + | 0.0309 0.0104 0.0224 0.0174 0.0188 0.0129 0.0027 0.0127
[5] 1 40001-50000 + | 0.0613 0.0217 0.0242 0.0347 0.03 0.0101 0.0025 0.0181
But for all tri/di/mononucleotide context. Any ideas? A
how did you get the output above ? what's wrong with this package ?
This is from the Fishhook package. Nothing wrong with it - it just does not show you how to generate nucleotide context for hg38.
http://mskilab.com/fishHook/tutorial.html
I've also asked the authors.