Hello, I have a fasta file containing 10 short DNA sequences (K-mers) which are significantly associated with a trait of interest. I want to map these sequences to a reference genome to identify the location and do some downstream analyses. I have used Bowtie v.1.2.2. to map the K-mers to the reference. First, I created the index for the reference genome. Then, I used the following command to get the output:
bowtie -f -a --best --strata reference_genome 1011_seq.fa > 1011_alignment
Here, I used -f
to indicate the input file which is 1011_seq.fa
that contains the K-mers. With this code, I get the output without any error message. The output looks like below:
Sequence_1 + 21 106906 AACGGAGACATGGGAACTAGAAGGA IIIIIIIIIIIIIIIIIIIIIIIII 0 8:G>C,17:C>T
Sequence_2 - 5 328003 ATCCCGCTCTTAGCGCATAGCTCGT IIIIIIIIIIIIIIIIIIIIIIIII 4 16:T>C,22:T>C
Sequence_2 + 3 3482001 ACGAGCTATGCGCTAAGAGCGGGAT IIIIIIIIIIIIIIIIIIIIIIIII 4 9:A>G,22:A>G
Sequence_2 + 9 1055399 ACGAGCTATGCGCTAAGAGCGGGAT IIIIIIIIIIIIIIIIIIIIIIIII 4 0:G>A,22:A>G
Sequence_2 + 3 996982 ACGAGCTATGCGCTAAGAGCGGGAT IIIIIIIIIIIIIIIIIIIIIIIII 4 0:G>A,22:A>G
Sequence_2 - 3 1050015 ATCCCGCTCTTAGCGCATAGCTCGT IIIIIIIIIIIIIIIIIIIIIIIII 4 9:T>C,22:T>C
Sequence_3 + 21 106907 ACGGAGACATGGGAACTAGAAGGAT IIIIIIIIIIIIIIIIIIIIIIIII 0 7:G>C,16:C>T
Sequence_4 + 21 106901 AGGTCAACGGAGACATGGGAACTAG IIIIIIIIIIIIIIIIIIIIIIIII 0 13:G>C,22:C>T
Sequence_5 - 21 106899 CGAGGTCAACGGAGACATGGGAACT IIIIIIIIIIIIIIIIIIIIIIIII 0 0:C>T,9:G>C
Sequence_6 + 21 106905 CAACGGAGACATGGGAACTAGAAGG IIIIIIIIIIIIIIIIIIIIIIIII 0 9:G>C,18:C>T
Sequence_7 - 3 3481999 TTACGAGCTATGCGCTAAGAGCGGG IIIIIIIIIIIIIIIIIIIIIIIII 4 0:A>G,13:A>G
Sequence_7 + 5 328005 CCCGCTCTTAGCGCATAGCTCGTAA IIIIIIIIIIIIIIIIIIIIIIIII 4 0:T>C,6:T>C
Can someone please tell me if the output is correct or not? I can recognize the strand sign, chromosome number, then the position and sequence. What I do no understand is the 6th and 7th columns. Why there is a continuous III and what does the number 0 and 4 means? Thanks a lot in advance.
Regards Anik
If this is really important to you, it may be wise to consider using the most recent version of bowtie. I have
v2.4.1
which still may not be the latest, but yours is definitely behind by several big upgrades.Mensur Dlakic : These are very short input sequences so
bowtie v.1.x
is the appropriate program to use.Oh okay. I will definitely check. Thanks for the info. I was just following a paper. Because I normally use Bowtie2.