Difference between revisions of "Re-sequencing"
From Crop Genomics Lab.
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|} | |} | ||
| + | 3. convert sam to bam | ||
| + | {| class="wikitable" | ||
| + | |- | ||
| + | | samtools view -Sb <SAMFILE> > <BAMFILE> | ||
| + | |} | ||
'''variation discovery''' | '''variation discovery''' | ||
Revision as of 05:31, 23 June 2014
bwa pipe
bowtie2 pipe
1. Make bowtie index
| bowtie2-build reference.fa reference.fa |
2. Align
| bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output |
3. convert sam to bam
| samtools view -Sb <SAMFILE> > <BAMFILE> |
variation discovery
