deletions | additions
diff --git a/notebooks/kmer-counting.ipynb b/notebooks/kmer-counting.ipynb
index b5c7094..fe3b6ef 100644
--- a/notebooks/kmer-counting.ipynb
+++ b/notebooks/kmer-counting.ipynb
...
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"commit
ea42e79505c9ad5e0f136037e2746abc4f7cd4c7\r\n", 2b4eef9ffd7530406816c30b281b635306a9b0db\r\n",
"Author: Ino de Bruijn \r\n",
"Date:
Mon Tue Jul
14 20:18:45 15 18:25:21 2014 +0200\r\n",
"\r\n",
"
Add jellyfish interface\r\n" Further work on counting kmers. Can output tsv now of contig with kmer origin percentage\r\n"
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"input": [
"jfr.write_refs_kmer_count_of_fasta(\"/media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/ref-jellyfish-test/low-purity/contigs-velvetnoscaf31-min500-purity-below-09.fa\",\n",
" 31,\n",
" \"/media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/ref-jellyfish-test/low-purity/val/contig-ref-kmer-composition-31.tsv\")"
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"Started at
18:00" 14:00"
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...
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"After inspecting output.\n",
"\n",
"- Low purity contains sometimes more false kmers than kmers from other species\n",
"- What is the LCA for each incorrect kmer? Maybe should be using Kraken instead"
]
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