Iso-Seq mapping to L1HS/PA2 consensus sequence
Raquel Garza
Published: 2024-03-15 DOI: 10.17504/protocols.io.5qpvorw7dv4o/v1
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Abstract
The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots
Steps
Mapping to L1HS/PA2 consensus sequence
1.
A L1HS and L1PA2 consensus sequence was used to create a minimap2 (version 2.24; RRID:SCR_018550) index
#L1 consensus index minimap2
minimap2 -d L1consensus.mmi L1consensus.fa
```to map FLNC reads (HiFi reads).
2.
The density of mapped reads was visualized in the Integrative Genomics Viewer (IgV) (version 2.12.3; RRID:SCR_011793)
3.
The number of mapped reads in the L1s 5’ UTR was retrieved using samtools view (-c) (version 1.9; RRID:SCR_002105), specifying the first 900 bp of the consensus sequence as the coordinates of interest.
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