benlangmead / bowtie-majref Goto Github PK
View Code? Open in Web Editor NEWScripts related to building major-allele references for Bowtie and Bowtie 2
License: MIT License
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akhileshkaushalbowtie-majref's Issues
Naming of chromosome M/MT
I'm using the grch38_1kgmaj.fa reference sequence and associated Bowtie2 index, but having a hard time understanding why chromosomes all use the standard Ensembl nomenclature (1, 2, X etc), except for Mitochondrial DNA: M (instead of MT in Ensembl).
Is this possibly a bug due to an overzealous sed command?
the ftp site links are switched in the README.md
Hi there. I noticed in the README that the ftp sites are switched:
| Bowtie 2 | GRCh38 + major SNPs | ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19_1kgmaj_bt2.zip |
|---|---|---|
| Bowtie 2 | hg19 + major SNPs | ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/grch38_1kgmaj_bt2.zip |
can you explain how to build this index?
Hi
I am curious about fasta+vcf index.
how to build this combined index?
please fill me in on the dirt.
Thanks.
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