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.