Open zznx opened 1 month ago
Hello,
--gbar <int> | Disallow gaps within <int> positions of the beginning or end of the read. Default: 4.
Given the following reference:
>a
GGAATATTTGCGATTTGCCATTTTCTCTCAAGAGT
and read:
>r1
GGAATAGCGATTTGCCATTTTCTCTCAAGAGT
Trying to align the read to reference will cause bowtie2
to report a gap in the alignment i.e.
in order to transform the reference to the read the 3 T
s, starting at position 7, would have
to be deleted from the reference (you can see this represented in the CIGAR as well as the MD:Z).
GGAATATTTGCGATTTGCCATTTTCTCTCAAGAGT
|||||| ||||||||||||||||||||||||||
GGAATA---GCGATTTGCCATTTTCTCTCAAGAGT
12345678901234567890123456789012345
./bowtie2-align-s -x /tmp/out -f read.fq -a --overhang --gbar 4
r1 0 a 1 255 6M3D26M * 0 0 GGAATAGCGATTTGCCATTTTCTCTCAAGAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:6^TTT26 YT:Z:UU
This gap happens within 6 bases of the start of the read so bowtie2 will report this alignment
as valid since it does not violate the default for --gbar
which is 4.
If we change --gbar
to 6 then bowtie2 will no longer consider this alignment as valid.
./bowtie2-align-s -x /tmp/out -f read.fq -a --overhang --gbar 6
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
@HD VN:1.5 SO:unsorted GO:query
@SQ SN:a LN:35
@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/home/rcharles/src/git/bowtie2/bowtie2-align-s -x /tmp/out -f read.fq -a --overhang --gbar 6"
r1 4 * 0 0 * * 0 0 GGAATAGCGATTTGCCATTTTCTCTCAAGAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
I will need to get back to you with an example explaining --dpad
. In the meantime I hope this helps.
Yes, I know what you mean, it's a kind of assumption that I think there should be no gap in the first four bases, or it's a rule summarized by a lot of data. Which one is it?
Hi, I'm reading the manual I don't know what's going on here, but if there's a problem, how can I solve it myself? Can you explain? Or provide relevant literature, thank you