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Mapping of CDS sequence of genes using minimap2

Hi, I have downloaded the CDS sequence of some Bos taurus genes from NCBI in fasta format. My goal is to view the different exons in IGV after mapping it to the reference genome. The problem now is that minimap2 (even after using the --splice option) is only mapping the first exon sequence. Does anyone know a way to map these reads which includes the splice junctions and hence all the exons in the gene. ADD INFO: when mapping and viewing the complete sequence it is mapping fine but the splice junctions are not properly marked hence it becomes hard to find the exact position of the exons.

minimap2 mapping fasta cds
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updated by lieven.sterck lieven.sterck • written by harisanjanas • harisanjanas

Hi! it's been a while but I'm just wondering whether you found any solution for this? thanks

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written by sina.majidian • sina.majidian

quite simple, use a different aligner :)

one I forgot to add earlier (years ago thus) but worth a look is BBmap (from the bbtools package). It might need some tinkering with the parameters to get the fasta input accepted though

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written by lieven.sterck lieven.sterck

1 answer

I suggest to have a look at the more 'old-school' mappers: GenomeThreader, GMAP, EST2genome, ... they are definitely slower than minimap but are very capable to identify (or correctly splice-map) CDS/cDNA sequences

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written by lieven.sterck lieven.sterck

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