Name: kmerizer
Owner: Hurwitz Lab
Description: Working with k-mers
Created: 2015-02-20 16:11:35.0
Updated: 2015-03-10 20:33:56.0
Pushed: 2015-07-27 03:47:04.0
Homepage: null
Size: 143
Language: Perl
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
Given an input file in FASTA format (set “test.fa”):
HWI-ST885:65:C07WUACXX:8:1101:1330:2049 1:Y:0:ACAGTG TTCTTTCTCTTCCTCCGGCTACTTAGATGTTTCAGTTCACCGGGTTCCCCTCCA TACCCTATGGATTCAGA HWI-ST885:65:C07WUACXX:8:1101:1267:2120 1:N:0:ACAGTG ATTCTCTGCGGCCTCTTTCGAGGCTCCCCTTTTTCCGAAGTTACGGGGTCAACT TGCCGAGTTCCTTAACAACCCTTCTCCCGTTGGCCTTAGGA
Create two files in “out” directory:
“.kmers” file of k-sized “mers” (contiguous letters)
“.locs” file read id and the number of k-mers in that read
The “.kmers” file is used with Jellyfish to query a suffix array. The output of that is the k-mer and the number of times it was seen. Then we'll use the “.locs” file to find match those lines with the read to calculate the mode.