steuernb / agrenseq Goto Github PK

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