ToAmos - Revision history

Floflooo: /* Known issues */

2011-03-17T08:58:06Z

‎Known issues

2011-03-17T08:57:27Z

‎Errors

2011-02-28T16:10:44Z

‎Errors

2010-12-14T18:12:30Z

‎Options: link for gde-like format contig file

2010-12-14T18:11:26Z

2010-12-14T18:06:40Z

The -i option is decribed in it's own section below

2010-12-14T18:04:05Z

‎Known issues

2010-12-14T18:02:47Z

‎Options

@@ Line 80: / Line 80: @@
 == Known issues ==
-The -ta (TIGR Assembler input) and -ace (ACE formatted input) options have not been throughly tested and likely do not properly work.  Contact us if either of these options is important to you.
+The -ta (TIGR Assembler input) option has not been thoroughly tested and likely does not properly work. Contact us if either of these options is important to you.
-−
 == Errors ==
 n/a

@@ Line 84: / Line 84: @@
 == Errors ==
- toAmos -c my.test.contig -m my.test.mates -o my.test.afg
+n/a
- Cannot find ID for sequence lid05.f
-−
-This problem is caused by forgetting to pass a fasta file (with -s) for the read sequences in the contig file. This is a bit weird as the reads are already in the .contig file.

← Older revision		Revision as of 16:10, 28 February 2011
Line 87:		Line 87:
	Cannot find ID for sequence lid05.f		Cannot find ID for sequence lid05.f

−	This problem is caused by...	+	This problem is caused by forgetting to pass a fasta file (with -s) for the read sequences in the contig file. This is a bit weird as the reads are already in the .contig file.

@@ Line 38: / Line 38: @@
   | -bq <good_qual>  || maximum quality score for  low-quality bases (default: 10) - if no quality file provided bases outside the clear range are assigned this quality value (default 10)
   |-
-  | -c <tigr_contig> || provide TIGR .contig file
+  | -c <tigr_contig> || provide TIGR .contig file [http://www.cbcb.umd.edu/research/contig_representation.shtml in GDE-like format]
   |-
   | -a <celera_asm>  || use Celera Assembler .asm contig file (contig and scaffold information)
@@ Line 46: / Line 46: @@
   | -utg             || include all UTG unitig messages in the .asm file as AMOS contigs
   |-
-  | -ta <tigr_asm>   || contig file in TIGR Assembler format (.tasm) [http://www.cbcb.umd.edu/research/contig_representation.shtml]
+  | -ta <tigr_asm>   || contig file in TIGR Assembler format (.tasm)
   |-
   | -ace <phrap_ace> || contig file in Phred ACE format (can be accompanied by -q)

@@ Line 46: / Line 46: @@
   | -utg             || include all UTG unitig messages in the .asm file as AMOS contigs
   |-
-  | -ta <tigr_asm>   || contig file in TIGR Assembler format (.tasm)
+  | -ta <tigr_asm>   || contig file in TIGR Assembler format (.tasm) [http://www.cbcb.umd.edu/research/contig_representation.shtml]
   |-
   | -ace <phrap_ace> || contig file in Phred ACE format (can be accompanied by -q)

@@ Line 63: / Line 63: @@
   |-
   | -scaff <bambus_scaff> || scaffold file in Bambus .scaff format
   |-
   | -map <dst_map>   || read map information - mapping from internal library ID to external library ID useful in conjunction with the -f option.  This file consists of space-separated records providing a mapping from the "acc:" field in "DST" records within the .frg file to an externally recognizable name for each library.

← Older revision		Revision as of 18:04, 14 December 2010
Line 83:		Line 83:

	The -ta (TIGR Assembler input) and -ace (ACE formatted input) options have not been throughly tested and likely do not properly work. Contact us if either of these options is important to you.		The -ta (TIGR Assembler input) and -ace (ACE formatted input) options have not been throughly tested and likely do not properly work. Contact us if either of these options is important to you.
		+
		+
		+	== Errors ==
		+	toAmos -c my.test.contig -m my.test.mates -o my.test.afg
		+	Cannot find ID for sequence lid05.f
		+
		+	This problem is caused by...

@@ Line 26: / Line 26: @@
 == Options ==
-{|
+{| class="somecssclass" border="1"
   |-
   | -o <out_file>    || output filename ('-' for standard output)