Contigs and scaffold in reference genome

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The Ensembl human reference genome sequence and annotation GTF/GFF contains contigs and scaffold apart from the chromosomes. Should they be removed prior to alignment of RNA-Seq reads or BS-Seq reads?

It might be useful to keep such sequences to see if any reads align to any region and subsequently detect gene expression/methylation. But it might also cause multimapping.


BWA


Ensembl


Genome


Reference


HiSat


NCBI

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