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
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