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License: GNU General Public License v3.0
Hi,
AgRenSeq is a really cool idea,and i now rerun your pipline with my test data,
count kmers from NLR contigs from 5 accessions, i create the Presence/Absense Matrix use this cmd:
java -jar AgRenSeq_CreatePresenceMatrix.jar -i accessions.txt -o AgRenSeq_k51_presencematrix.txt -t 1 -n 1
and my outputmatrix.txt seem like this:
#x80,x81,x82,x83,x84
AGATGGGCGAGACGTAAGATGACTGAAAATAACTTCTCGCTGTTCTTACGG 111
CTTCTCCCTCCCGGTGTGCTTCCTGGCGGCGGGCACGAACACGCGGTCGTA 00011
CATCACAGTCTGTTCTTGGCTAGCTTCGATCTGTGAATTTGGTGCAGAAGC 01
ACGGGCGTATGTTTCTCGAGCGAATTCGATCCGGCACCGGCGCACGGCGAA 00001
ATGTATTGTCGTTAAGGACCGATGGGTCCATGATTATCTTACAGTGCGACC 01
CAAACAGTTAGGCCTGGTAATTTTGATAGTGCAGCATCACCTAGATCTGCA 11011
AGGCAGTACAAGGGGGTGAGGATGCGGAGCTGGGGGTCGTGGGTGTCGGAG 0001
ACAAATACCACTACTTTTCATTCAACTTAAAACACAAAGTCATTTTTGGTG 10011
CCTTAATCAGCTACCATCTCATGCCATGCTACTTGCTTTCAGTCACTGTAG 00101
why some kmers don't have 0/1 tags
many thanks
Why not have the AgRenSeq_CreatePresenceMatrix.jar, I can not
find it in src
hope answer the question
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