Making slices from BAM files - Revision history

Hjmegens at 13:21, 14 March 2012

2012-03-14T13:21:29Z

← Older revision		Revision as of 15:21, 14 March 2012
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	This article describes how to automate the creation of slices from a collection of BAM files. This procedure assumes that all BAM files are together in a single folder.		This article describes how to automate the creation of slices from a collection of BAM files. This procedure assumes that all BAM files are together in a single folder.

	== ~~variable~~ that points to the collection of bam files ==		== Variable that points to the collection of bam files ==
	First, make a variable BAMDIR that holds the path to the BAM files:		First, make a variable BAMDIR that holds the path to the BAM files:
	<source lang='bash'>		<source lang='bash'>
	BAMDIR='/shared/Sus/BAM_files_hjm_newbuild10_2/'		BAMDIR='/shared/Sus/BAM_files_hjm_newbuild10_2/'
	</source>		</source>
	== ~~create~~ a variable with all your bamfile names ==		== Create a variable with all your bamfile names ==
	Then create a variable, BAMFILE, that holds all the names of the BAM files:		Then create a variable, BAMFILE, that holds all the names of the BAM files:
	<source lang='bash'>		<source lang='bash'>
Line 12:		Line 12:
	</source>		</source>

	== ~~check~~ that your variable contains valid information ==		== Check that your variable contains valid information ==
	Optional: if you are not sure that everything went ok, you can of course always check what values your variable contains:		Optional: if you are not sure that everything went ok, you can of course always check what values your variable contains:
	<source lang='bash'>		<source lang='bash'>
	echo $BAMFILE		echo $BAMFILE
	</source>		</source>
	== ~~make~~ a slice for each bamfile ==		== Make a slice for each bamfile ==
	The slices can then simply be extracted by a shell one-liner. It assumes that samtools is installed and in your path. The example here would slice out the region containing the KIT gene in Sus scrofa build 10.2.		The slices can then simply be extracted by a shell one-liner. It assumes that samtools is installed and in your path. The example here would slice out the region containing the KIT gene in Sus scrofa build 10.2.
	<source lang='bash'>		<source lang='bash'>

Hjmegens at 10:54, 7 March 2012

2012-03-07T10:54:37Z

← Older revision		Revision as of 12:54, 7 March 2012
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			This article describes how to automate the creation of slices from a collection of BAM files. This procedure assumes that all BAM files are together in a single folder.

			== variable that points to the collection of bam files ==
			First, make a variable BAMDIR that holds the path to the BAM files:
			<source lang='bash'>
			BAMDIR='/shared/Sus/BAM_files_hjm_newbuild10_2/'
			</source>
	== create a variable with all your bamfile names ==		== create a variable with all your bamfile names ==
			Then create a variable, BAMFILE, that holds all the names of the BAM files:
	<source lang='bash'>		<source lang='bash'>
	BAMFILE=`ls $BAMDIR*.bam \| sed 's/.\+\///' \| sed 's/.bam//'`		BAMFILE=`ls $BAMDIR*.bam \| sed 's/.\+\///' \| sed 's/.bam//'`
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	== check that your variable contains valid information ==		== check that your variable contains valid information ==
			Optional: if you are not sure that everything went ok, you can of course always check what values your variable contains:
	<source lang='bash'>		<source lang='bash'>
	echo $BAMFILE		echo $BAMFILE
	</source>		</source>
	== make a slice for each bamfile ==		== make a slice for each bamfile ==
			The slices can then simply be extracted by a shell one-liner. It assumes that samtools is installed and in your path. The example here would slice out the region containing the KIT gene in Sus scrofa build 10.2.
	<source lang='bash'>		<source lang='bash'>
	for i in $BAMFILE;		for i in $BAMFILE;
	do echo $i;		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 ;		samtools view -b $BAMDIR$i.bam Ssc10_2_8:43212683-43981653 >$i.SSC8_43212683-43981653.bam ;
	done		done
	</source>		</source>

Hjmegens at 10:47, 7 March 2012

2012-03-07T10:47:23Z

← Older revision		Revision as of 12:47, 7 March 2012
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	<source lang='bash'>		<source lang='bash'>
	BAMFILE=`ls *.bam \| sed 's/.bam//'`		BAMFILE=`ls $BAMDIR*.bam \| sed 's/.\+\///' \| sed 's/.bam//'`
	</source>		</source>

Hjmegens at 10:43, 7 March 2012

2012-03-07T10:43:27Z

@@ Line 1: / Line 1: @@
 <source lang='bash'>
 BAMFILE=`ls *.bam | sed 's/.bam//'`
 </source>

Hjmegens: Created page with " BAMFILE=`ls *.bam | sed 's/.bam//'` "

2012-03-07T10:40:06Z

Created page with "<source lang='bash'> BAMFILE=`ls *.bam | sed 's/.bam//'` </source>"

New page

<source lang='bash'>
BAMFILE=`ls *.bam | sed 's/.bam//'`
</source>