thegenemyers
commented
7 years ago Yes, that's not right. Its good that Damapper finds both matches, but it should not be a chain. Any chance you could send me a minimal example that produces the problem? For example, if building a DAM for read 6661 and another for read 109492, and comparing produced the problem then sending me .fasta's of the two reads would suffice to let me reproduce the problem. (You can produce a .fasta of one or more reads in a DB or DAM with "DBshow"). Please advise. -- Gene
On 5/18/17, 1:58 AM, Eugene Goltsman wrote:
Hello, I'm trying out DAMAPPER for mapping a set of unitigs to PacBio reads, and when parsing the results I notice that sometimes duplicate alignments to different parts of the same read are reported as chains, which seems like not the intended behavior. Perhaps this has to do with the fact that I'm aligning short sequences to long reads, and not vice versa? Here's an example from the LAdump -lc output:
P 6661 109492 n > L 83 12383 C 0 83 11853 11937 P 6661 109492 n - L 83 12383 C 0 83 11948 12032
Here, the query contig '83' aligned fully to two locations on read '109492', which should probably be reported as two separate LAs, and not as a chain.
Eugene G
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egoltsman
Hello, I'm trying out DAMAPPER for mapping a set of unitigs to PacBio reads, and when parsing the results I notice that sometimes duplicate alignments to different parts of the same read are reported as chains, which seems like not the intended behavior. Perhaps this has to do with the fact that I'm aligning short sequences to long reads, and not vice versa? Here's an example from the LAdump -lc output:
P 6661 109492 n > L 83 12383 C 0 83 11853 11937 P 6661 109492 n - L 83 12383 C 0 83 11948 12032
Here, the query contig '83' aligned fully to two locations on read '109492', which should probably be reported as two separate LAs, and not as a chain.
Eugene G