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Question: GRCH37 vs hg19 vs B37 vs canonincal
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gravatar for shamsher jagat
14 months ago by
shamsher jagat • 590
United States
shamsher jagat • 590 wrote:

In galaxy which human genome should be compatible with GRCH37 annotation for alignment. I uploaded fastq with GRCH37 genome, when I look at alignment options with HISAt it offers- b37/ hg19 canonical/ hg19 male/ female. Which genome should be used so that it should be compatible with GRCH37 annotation. Thanks
rna-seq • 1.1k views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by shamsher jagat • 590
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The genomes hg19 (source UCSC) and hg_g1k_v37 (source GATK) are both based on the baseline GRCH37 assembly. The difference is in the chromosome identifiers.

hg19 example chromosome identifiers:

chr1
chr2
..
chrX
chrY
chrM

hg_g1k_v37 example chromosome identifiers:

1
2
..
X
Y
MT

Compare the identifiers in your GRCH37 annotation to the above (or the full source dataset) to determine the correct one to use.

FAQ (includes a description for built-in genome variants): https://galaxyproject.org/support/chrom-identifiers/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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