Comments (4)
cmdcolin
commented on May 27, 2024
it looks like there is no fasta index for this file e.g. https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz.fai does not exist (interestingly https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz.gzi does exist, but both the fai and gzi are needed for bgzip indexed fasta)
you can maybe use https://jbrowse.org/genomes/CHM13/fasta/chm13v2.0.fa.gz instead, we created this for testing purposes but should be somewhat stable and it has fai and gzi
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cmdcolin
commented on May 27, 2024
(there is a gfftabix here also https://jbrowse.org/genomes/CHM13/gff/chm13v2.0.gff.gz)
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arpanda
commented on May 27, 2024
Thanks @cmdcolin.
I can browse the chm13 genome now. is there any aliases file for chm13 in that link?
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cmdcolin
commented on May 27, 2024
might be able to use https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txt as alias, hs1 from ucsc is same as chm13v2.0
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Related Issues (20)
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