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.
•
written
by
saranpons3
0 answers
No answers yet.
Log in to answer this question.
-
Issue using MaSuRCA-3.2.6
written by Chvatil
I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Thanks. I'll follow this hereafter
Where are the
AAAAAAAcoming from? You also seem to have mismatch among bases and quality values in the example reads you have posted.Resisting urge to make Monty Python reference.
Op wrote it is toy data.
OP also said
So I assume the example posted is what was used to run BFCounter.
Sorry for mismatch. While posting here i missed including entire line. The following is the correct line
GFGGDGGFGGGG@GFGGFG@EFDFFEGFDE?>BC9>.:*>8<4
Hello saranpons3!
Duplicate posting: C: Can anybody explain what this statement says?
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
Wouldn't it be better to leave the question open and remove the comment?
The comment in other thread has a couple of responses.
saranpons3 : If you want to keep this as a separate question then put a link for this post in the other thread mentioned above. We can then open this question back up.
Hello genomax2, I would like to keep this question as a separate one. So i will put a link for this post in the other thread.
Since you have not put a link for this thread in other post I am going to leave this question closed for new answers.
You could try a different software like jellyfish and compare the results, that will give you a better idea what is correct.
Ok I will try with other k-mer counters. But I'm wondering that why I'm not getting proper output from BFCounter.