Making slices from BAM files: Difference between revisions
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(Created page with "<source lang='bash'> BAMFILE=`ls *.bam | sed 's/.bam//'` </source>") |
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== create a variable with all your bamfile names == | |||
<source lang='bash'> | <source lang='bash'> | ||
BAMFILE=`ls *.bam | sed 's/.bam//'` | BAMFILE=`ls *.bam | sed 's/.bam//'` | ||
</source> | |||
== check that your variable contains valid information == | |||
<source lang='bash'> | |||
echo $BAMFILE | |||
</source> | |||
== make a slice for each bamfile == | |||
<source lang='bash'> | |||
for i in $BAMFILE; | |||
do echo $i; | |||
samtools view -b /shared/Sus/BAM_files_hjm_newbuild10_2/$i.bam Ssc10_2_8:43212683-43981653 >$i.SSC8_43212683-43981653.bam ; | |||
done | |||
</source> | </source> | ||
Revision as of 11:43, 7 March 2012
create a variable with all your bamfile names
<source lang='bash'> BAMFILE=`ls *.bam | sed 's/.bam//'` </source>
check that your variable contains valid information
<source lang='bash'> echo $BAMFILE </source>
make a slice for each bamfile
<source lang='bash'> for i in $BAMFILE;
do echo $i; samtools view -b /shared/Sus/BAM_files_hjm_newbuild10_2/$i.bam Ssc10_2_8:43212683-43981653 >$i.SSC8_43212683-43981653.bam ;
done </source>