[maker-devel] map2assembly

Carson Holt carsonhh at gmail.com
Mon Nov 10 09:12:53 MST 2014


You can also use the -l option when running gff3_merge to correct for for unique IDs when merging multiple GFF3 files (i.e. IDs will be uniq within a file, but may not be unique across files when mapping transcripts the IDs are being copied direct from the aligned transcript).

—Carson


> On Nov 10, 2014, at 9:08 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> Try using the transcript score (column 6).  It should indicate the % recovery. A 100 means perfect match to the input transcript.  The value is %identity multiplied by %coverage, so it will decrease because of a lack of identity or a lack of end-to-end alignment.
> 
> —Carson
> 
> 
> 
> 
> 
>> On Nov 10, 2014, at 8:54 AM, Michael Thon <mike.thon at gmail.com> wrote:
>> 
>> Hi - 
>> We’re using map2assembly to map genes from other gene annotation pipelines onto the genome sequence in order to compare AED values to a maker de novo annotation.  We found a few transcripts that map2assembly maps to multiple loci in the genome.  Is there any way to know if these are all equally good alignments or are they all above some present threshold? I’m trying to decide what to do with the multiple mappings - whether we should discard all but one (in that case we’d need to decide which one) or whether we should keep them all.  Keeping them all makes the most sense but the problem is they all have the same id. should map2assembly append a number to the id when a transcript maps to multiple locations in the genome?
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