Contigs and scaffold in reference genome
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9 weeks ago
Arindam Ghosh ▴ 380

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 • 212 views
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That give an idea that I am atleast using the correct file - the PRIMARY sequence. But it is in the primary sequence that contains Chr1-22, X, Y, MT and a few others. So do i keep these few other sequences or not?

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For normal RNAseq you can keep everything in primary sequence.

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