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Old 01-30-2016, 11:42 AM   #1
Yasmin Lima
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Location: Brasília, Brazil

Join Date: Jan 2016
Posts: 2
Default tmap aligers reference genome

Hi everyone,
I would like to know how is the default reference genome used in TMAP aligner.
I thought it was Human Genome - Feb. 2009 (hg19, GRCh37) that is in Ion Community documentation, but they don't match with my data.
The bam file used contigs 1, .., X, Y, MT, and GL###, but the reference used chr1,crh2, …, chrX, chrY, chrM. They do not appear to be the same.

Thank you!
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Old 01-30-2016, 03:16 PM   #2
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Location: uk

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Posts: 666

UCSC and Ensembl use different naming conventions for the chromosomes.

Ensembl uses 1, 2, 3, etc, and UCSC uses chr1, chr2, chr3, etc.
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