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tue.txt
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tue.txt
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#build bwa index from horse fasta
#align bat reference fasta to horse index
#identify reads in x-chromosome and y-chromosome
#identify positions of reads
#filter out SNPs that fall in those reads
#making index from horse (within /leo/devon/projects/batgenome/nonbatfasta):
bwa index horse.fa.gz
#align bat reference to horse:
bwa mem \
/leo/devon/projects/batgenome/nonbatfasta/horse.fa.gz \
/leo/devon/projects/batgenome/FastaBat/mylu.fa > \
/leo/devon/projects/batgenome/refAligns2nonBat/myluRef_horse.sam
#convert sam to bam
#pull out .bam reads associated with X-chromosome
#
........
#what about pulling out just X and Y chromosomes from multiple species (cow, horse, sheep, pig) and creating a fasta of those sequences, then creating an index of those, then align MYLU to that?
IDEA:
once you get the genomes from your bats back... can you look at core/unique gene regions like in Roary with bacteria?
ftp://ftp.ensembl.org/pub/release-89/fasta/bos_taurus/dna/Bos_taurus.UMD3.1.dna.chromosome.X.fa.gz
#look up ScriptSeq v2 from (now) Illumina (frm. Epicetner)
...want to use a targeted enrichment first
#tandy warnow
"scaling statistical multiple sequence alignment to large datasets" (paper BMC Genomics)
.....
#MaFFT
##install