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steuernb / AgRenSeq

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empty columns in outputMatrix #1

Closed DengHAU closed 6 years ago

DengHAU commented 6 years ago

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

steuernb commented 6 years ago

Hi, Trailing zeros are omitted to save space. You know from the first line how many accessions you have. So, if you have 5, then a “111” is actually “11100” Cheers Burkhard

From: DengHAU notifications@github.com Reply-To: steuernb/AgRenSeq reply@reply.github.com Date: Friday, 30 March 2018 at 11:09 To: steuernb/AgRenSeq AgRenSeq@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [steuernb/AgRenSeq] empty columns in outputMatrix (#1)

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

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DengHAU commented 6 years ago

Thank you for your reply, your cool software works well.