search

thegenemyers / DALIGNER

Find all significant local alignments between reads
Other
138 stars 61 forks source link

Mutual containment #69

Closed gt1 closed 6 years ago

gt1 commented 6 years ago

Hello Gene,

I see the following as an output of daligner/LAshow:

1 2 n [ 1..8,696> x < 0..8,990> ~ 23.00% (8,990 x 8,696 bps,2,034 diffs, 87 trace pts) 2 1 n < 0..8,990> x [ 1..8,696> ~ 23.00% (8,696 x 8,990 bps,2,034 diffs, 90 trace pts)

I wonder if this worked as intended. I thought daligner would try to extend alignments to the end of a read (in this case both) if it was close to an end, even if that meant lowering the score by that extension.

Best, German

thegenemyers commented 6 years ago

Yes, this is strange -- it should have extended to the end. Any chance you can send me .fasta's of the two reads? -- Gene

On 10/20/17, 12:48 PM, German Tischler wrote:

Hello Gene,

I see the following as an output of daligner/LAshow:

1 2 n [ 1..8,696> x < 0..8,990> ~ 23.00% (8,990 x 8,696 bps,2,034 diffs, 87 trace pts) 2 1 n < 0..8,990> x [ 1..8,696> ~ 23.00% (8,696 x 8,990 bps,2,034 diffs, 90 trace pts)

I wonder if this worked as intended. I thought daligner would try to extend alignments to the end of a read (in this case both) if it was close to an end, even if that meant lowering the score by that extension.

Best, German

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/thegenemyers/DALIGNER/issues/69, or mute the thread https://github.com/notifications/unsubscribe-auth/AGkkNj0zl0matTOXLBjBS6kJVSuaY77Uks5suHpwgaJpZM4QAgBa.