9 lines
369 B
Plaintext
9 lines
369 B
Plaintext
Download SRA reads in the FASTQ format
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for i in `awk '{if(NR != 1) print $4}' SraRunInfo.txt`; do fastq-dump --gzip $i; done
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for i in `ls *.gz`; do echo $i; ../../../../hisat2 --no-hd -x ../hla.graph -U $i --max-altstried 64 2> /dev/null | grep "A\*B" >> temp; done
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scripts/get_haplotype_ILMN_StrandSeq.py ILMN_StrandSeq/SraRunInfo.txt ILMN_StrandSeq/temp
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