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lh3/NA12878-DirectRNA-CustomTrack.md

Last active December 3, 2017 03:40
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NA12878-DirectRNA-CustomTrack.md

NA12878 DirectRNA reads were obtained here (passed reads only) and aligned with minimap2 v2.5 against the no_alt_analysis_set of GRCh38 plus SIRV contigs. It took <1 wall-clock hour across 16 CPU cores with command-line options: -cx splice -k14 --cs -uf -N20 -t16. Alignments were converted to BED with the misc/splice2bed.js script from minimap2 and then converted to BigBed. Ribosome-related genes (RPL*, RPS*, EEF* and RPSA) were excluded to reduce the file size. The final BigBed is hosted at OSF.

A UCSC custom track is configured with

track type=bigBed name=NA12878-DirectRNA.minimap2-2.5 useScore=1 visibility=4 itemRgb="On" bigDataUrl=https://files.osf.io/v1/resources/b5nm2/providers/osfstorage/5a2347599ad5a10272ed5739?action=download&version=1&direct

You can access this track with the following link. A GMAP alignment track is temporarily available here. This track contains 1/4 of reads. GMAP is still running. It will take 4–5 wall-clock days to finish using 16 CPU cores.

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