Off topic:Not able to understand BFCounter result!!!
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7.0 years ago
saranpons3 ▴ 70

Hello Members, I tried to run BFCounter which is a k-mer counter software on the following fastq data set which contains only 2 reads and each read of length 49 bp. (This data set is a toy data set I'm using to understand BFCounter).

@SRR292770.1 FCB067LABXX:4:1101:1155:2103/1
GGAGTCATCATACGGCGCTGATCGAGACCGCAACGACTTTAAGGTCGCA 
+ 
FFFFCFGDCGGGFCGBGFFFAEGFG;B7A@GEFBFGGFFGFGEFCFFFB 
@SRR292770.3 FCB067LABXX:4:1101:1166:2158/1 
GGAGTCATCATACGGCGCTGATCGAGACCGCAACGACTTTAAGGTCGCA 
+ 
GFGGDGGFGGGG@GFGGFG@EFDFFEGFDE?>BC9>.:*>8<4

When i ran BFCounter on the data set, value, I've chosen for k-mer is 25. As there are 49 bp in a read, total number of k-mers to be generated should be 25 as there are 25 distinct k-mers and I'm getting 25 k-mers from BFCounter. The output of BFCounter is as follows.

AAAAAAAAAAAAGTTGTTCTCGTCC 2 
GCGACCTTAAAGTCGTGACGGACGA 2 
CGTCCGTCACGACTTTAAGGTCGCA 2 
GACCTTAAAGTCGTGACGGACGAGA 2 
AAAAAAAAAAAAAAAAGTTGTTCTC 2 
AAAAAGTTGTTCTCGTCCGTCACGA 2 
AAAAAAAAAAAAAAGTTGTTCTCGT 2 
AAAAAAAAAAAGTTGTTCTCGTCCG 2 
AAAAAAAAAAGTTGTTCTCGTCCGT 2 
AAAAAAAAGTTGTTCTCGTCCGTCA 2 
AAAAAAGTTGTTCTCGTCCGTCACG 2 
GTTGTTCTCGTCCGTCACGACTTTA 2 
AAAAGTTGTTCTCGTCCGTCACGAC 2 
AAAAAAAAAAAAAAAGTTGTTCTCG 2 
ACCTTAAAGTCGTGACGGACGAGAA 2 
AAAGTTGTTCTCGTCCGTCACGACT 2 
AAAGTCGTGACGGACGAGAACAACT 2 
CCTTAAAGTCGTGACGGACGAGAAC 2 
AAAAAAAAAGTTGTTCTCGTCCGTC 2 
AAAAAAAGTTGTTCTCGTCCGTCAC 2 
AAGTCGTGACGGACGAGAACAACTT 2 
AAAAAAAAAAAAAGTTGTTCTCGTC 2 
CGACCTTAAAGTCGTGACGGACGAG 2 
CTTAAAGTCGTGACGGACGAGAACA 2 
TTAAAGTCGTGACGGACGAGAACAA 2

The number of k-mers BFcounter produsing is 25 and it is correct. But when i looked at k-mer content i don't feel they are correct and proper one. Can you tell me why this difference?

Thanks in advance.

BFCounter Kmer Counter • 845 views
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