Timeline for What is the tRNA gene copy variation between different yeast strains?
Current License: CC BY-SA 3.0
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| Feb 27, 2012 at 8:03 | history | bounty ended | Greg Slodkowicz | ||
| Feb 27, 2012 at 8:03 | comment | added | Greg Slodkowicz | I don't think the coverage is deep enough (1-4x) for de novo assembly but I'll try running tRNAscan-SE on the unassembled reads and maybe try to see if there's a difference in coverage of some tRNA genes which would suggest that duplicated genes have been mapped on the same locus. | |
| Feb 24, 2012 at 14:26 | comment | added | Larry_Parnell | I like @bobthejoe 's suggestion. I never intended that tRNAscan-SE would be run against an assembled genome. Depending on the size of your reads vs. the size of a typical tRNA gene, you may be able to input the reads themselves into tRNAscan-SE. If coverage of each genome is deep enough, try that de novo ass0embly. Also run the unassembled reads from each strain through tRANscan-SE - perhaps these are indeed those extra copies of the tRNA genes you're searching. Lastly, are there any gaps in an assembly where known tRNA genes are? I still think my suggestion would work. | |
| Feb 24, 2012 at 10:32 | comment | added | bobthejoe | It sounds like you should try a De Novo assembly. That might be tricky since you don't have any paired-end data but that might be able to discover any novel contigs. | |
| Feb 24, 2012 at 9:17 | comment | added | Greg Slodkowicz | I don't think this will work since it's NGS data assembled against a reference genome. In fact I ran tRNAscan-SE and all strains have exactly the same tRNA GCN as the reference strains but this is a consequence of the assembly process. | |
| Feb 23, 2012 at 15:04 | history | answered | Larry_Parnell | CC BY-SA 3.0 |