Mikko Rautiainen
Mikko Rautiainen
Which parameters did you use?
I couldn't reproduce this bug using either compiled from source or bioconda installation. Could you please try the installing via bioconda, or compiling from source, instead of biocontainer? About the...
Hi Juan, Currently there's no recommended parameters for mapping CCS reads to a large graph. For a small graph (multiple megabases) you can try `--seeds-first-full-rows 64 -b 35` which is...
Hi, could you upload the graph and the read?
Sounds like there is something weird going on with GraphAligner parsing the graph. Could you please upload the graph?
Hi, I think this should work if you have just one alignment per read: ``` cut -f 1,6 < alignments.gaf | awk '{print "P\t" $1 "\t" $2 "\t" "*";}' |...
Hi, the test graph doesn't have a path for >N1>N2>N3N9. The bandage screenshot below shows the topology of the graph. In this case GraphAligner does not merge the three alignments...
Doesn't exist as far as I know. Shouldn't be too difficult except for two conceptual questions. How should you handle partial alignments whose merge doesn't create a path, eg the...
> Is there any way to convince GraphAligner to drive through them rather than consuming the entire query sequence while aligning to them? No easy way as far as I...
Hi, could you please upload the graph and the read?