Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/samtools-0.1.16/examples/00README.txt @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/samtools-0.1.16/examples/00README.txt Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,23 @@ +File ex1.fa contains two sequences cut from the human genome +build36. They were exatracted with command: + + samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550 + +Sequence names were changed manually for simplicity. File ex1.sam.gz +contains MAQ alignments exatracted with: + + (samtools view NA18507_maq.bam 2:2044001-2045500; + samtools view NA18507_maq.bam 20:68001-69500) + +and processed with `samtools fixmate' to make it self-consistent as a +standalone alignment. + +To try samtools, you may run the following commands: + + samtools faidx ex1.fa # index the reference FASTA + samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM + samtools index ex1.bam # index BAM + samtools tview ex1.bam ex1.fa # view alignment + samtools pileup -cf ex1.fa ex1.bam # pileup and consensus + samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz +