Bowtie - Revision history

Rf at 11:04, 15 December 2016

2016-12-15T11:04:08Z

2016-12-02T14:27:26Z

2016-11-15T12:43:51Z

2016-11-15T12:38:25Z

2016-11-15T12:38:02Z

2016-11-15T12:36:32Z

2016-11-15T12:34:59Z

2016-11-15T12:27:16Z

2016-11-15T12:06:58Z

2016-11-15T12:02:31Z

@@ Line 17: / Line 17: @@
 == colorspace indexing ==
-A big advantage of this first version of bowtie is its ability to handle colorspace fastq files. For thsi, a special index of the reference sequence must be generated, using '''bowtie-build''' and the special option '''-C'''. The rest of the command is the same, and you would of course use a different label for later processing with colorspace files.
+A big advantage of this first version of bowtie is its ability to handle colorspace fastq files. For this, a special index of the reference sequence must be generated, using '''bowtie-build''' and the special option '''-C'''. The rest of the command is the same, and you would of course use a different label for later processing with colorspace files.
 = the alignment step =

← Older revision		Revision as of 14:27, 2 December 2016
Line 25:		Line 25:
	bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>		bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>

−	As you can see ~~we have three~~ arguments ~~here~~.	+	For example, in one recent run:
		+
		+	bowtie -S -C mabsref SRR1501363_.fastq bwt363go.sam
		+
		+	As you can see, the final two arguments are not marked by an ption, so always must be the uncompressed input fasta file and the output sam.

← Older revision		Revision as of 12:43, 15 November 2016
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	bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>		bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>
		+
		+	As you can see we have three arguments here.

@@ Line 21: / Line 21: @@
 = the alignment step =
-We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not   colorspace files. Here is an example run:
+We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not   colorspace files. Here is an template for such a command:
   bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>

← Older revision		Revision as of 12:38, 15 November 2016
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	We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not colorspace files. Here is an example run:		We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not colorspace files. Here is an example run:

−	bowtie -S -C ~~mabsref SRR1501363_.fastq bwt363go.sam~~	+	bowtie -S -C <label_for_index_of_reference> <uncompressed_fastq_filename> <output_filename_with_sam_extension>

← Older revision		Revision as of 12:36, 15 November 2016
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	= the alignment step =		= the alignment step =

−	We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not colorspace files.	+	We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not colorspace files. Here is an example run:
		+
		+	bowtie -S -C mabsref SRR1501363_.fastq bwt363go.sam

← Older revision		Revision as of 12:34, 15 November 2016
Line 18:		Line 18:

	A big advantage of this first version of bowtie is its ability to handle colorspace fastq files. For thsi, a special index of the reference sequence must be generated, using '''bowtie-build''' and the special option '''-C'''. The rest of the command is the same, and you would of course use a different label for later processing with colorspace files.		A big advantage of this first version of bowtie is its ability to handle colorspace fastq files. For thsi, a special index of the reference sequence must be generated, using '''bowtie-build''' and the special option '''-C'''. The rest of the command is the same, and you would of course use a different label for later processing with colorspace files.
		+
		+	= the alignment step =
		+
		+	We shall deal with colorspace files here, because there is only an added '''-C''' in the options for them, and so it can be ommited when they are not colorspace files.

@@ Line 1: / Line 1: @@
 = Introduction =
-This article refers to the early version of bowtie, which in fact has a few features that version 2 does not have, such as colorspace data processing
+This article refers to the early version of bowtie, which in fact has a few features that version 2 does not have, such as colorspace data processing.
 = Indexing the reference =
@@ Line 14: / Line 14: @@
 * the second argument is a label for the output index files, in this case '''e_coli_O157_H7'''
 * The extensions of the output files will have the extension '''ebwt'''. The root name will be the label mentioned above with  some changing added characters (1, 2, 3, 4, rev.1, rev.2)

@@ Line 13: / Line 13: @@
 * in this example '''NC_002127.fna''' is our reference and is the first argument
 * the second argument is a label for the output index files, in this case '''e_coli_O157_H7'''
-* The extensions of the output files will have the extension '''ebwt'''. The root name will be the label mentioned above with some changing added characters.
+* The extensions of the output files will have the extension '''ebwt'''. The root name will be the label mentioned above with  some changing added characters (1, 2, 3, 4, rev.1, rev.2)

← Older revision		Revision as of 12:02, 15 November 2016
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	bowtie-build NC_002127.fna e_coli_O157_H7		bowtie-build NC_002127.fna e_coli_O157_H7

−	~~Output~~ files will have the extension '''ebwt'''.	+	<ins>Explanation</ins>:
		+	* '''bowtie-build''' is indexing creation tol of bowtie
		+	* in this example '''NC_002127.fna''' is our reference and is the first argument
		+	* the second argument is a label for the output index files, in this case '''e_coli_O157_H7'''
		+	* The extensions of the output files will have the extension '''ebwt'''. The root name will be the label mentioned above with some changing added characters.