mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup [2015/11/18 19:25] – mkatari | mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup [2015/11/18 19:48] (current) – mkatari | ||
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| Line 20: | Line 20: | ||
| * remove duplicates | * remove duplicates | ||
| * create a bam index for dedup bam files | * create a bam index for dedup bam files | ||
| + | |||
| + | < | ||
| + | bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam | ||
| + | samtools view -bS Cohen.sam > Cohen.bam | ||
| + | samtools sort Cohen.bam Cohen_sorted | ||
| + | samtools index Cohen_sorted.bam | ||
| + | </ | ||
| + | |||
| For further curation | For further curation | ||
| Line 37: | Line 45: | ||
| - | < | ||
| - | bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam | ||
| - | samtools view -bS Cohen.sam > Cohen.bam | ||
| - | samtools sort | ||
| - | </ | ||
| < | < | ||
mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup.1447874703.txt.gz · Last modified: 2015/11/18 19:25 by mkatari