- N options with maq 0.7.1

seq_GA · 06-09-2009, 08:00 PM

why -N option is not working? I am not able to print mismatch positions?

Anyone has used - N options with maq 0.7.1? Please clarify whether this option is available. It always prints 0 at the last column of mapview results in text format. Thanks.

When I execute ./maq map, I get the options as below:

Usage: maq map [options] <out.map> <chr.bfa> <reads_1.bfq> [reads_2.bfq]
Options: -1 INT length of the first read (<=127) [0]
-2 INT length of the second read (<=127) [0]
-m FLOAT rate of difference between reads and references [0.001]
-e INT maximum allowed sum of qualities of mismatches [70]
-d FILE adapter sequence file [null]
-a INT max distance between two paired reads [250]
-A INT max distance between two RF paired reads [0]
-n INT number of mismatches in the first 24bp [2]
-M c|g methylation alignment mode [null]
-u FILE dump unmapped and poorly aligned reads to FILE [null]
-H FILE dump multiple/all 01-mismatch hits to FILE [null]
-C INT max number of hits to output. >512 for all 01 hits. [250]
-s INT seed for random number generator [random]
-W disable Smith-Waterman alignment
-t trim all reads (usually not recommended)
-c match in the colorspace
Anyone knows that whether maq 0.7.1 has -N options working or do I have start using maq 0.6.8?

Thanks.

pengchy · 10-21-2011, 04:14 AM

I wonder how -e will influence the results? How much should I set for the 100pe reads.

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06-09-2009, 08:00 PM	#1
seq_GA Senior Member Location: Asiana Join Date: Feb 2009 Posts: 124	- N options with maq 0.7.1 why -N option is not working? I am not able to print mismatch positions? Anyone has used - N options with maq 0.7.1? Please clarify whether this option is available. It always prints 0 at the last column of mapview results in text format. Thanks. When I execute ./maq map, I get the options as below: Usage: maq map [options] <out.map> <chr.bfa> <reads_1.bfq> [reads_2.bfq] Options: -1 INT length of the first read (<=127) [0] -2 INT length of the second read (<=127) [0] -m FLOAT rate of difference between reads and references [0.001] -e INT maximum allowed sum of qualities of mismatches [70] -d FILE adapter sequence file [null] -a INT max distance between two paired reads [250] -A INT max distance between two RF paired reads [0] -n INT number of mismatches in the first 24bp [2] -M c\|g methylation alignment mode [null] -u FILE dump unmapped and poorly aligned reads to FILE [null] -H FILE dump multiple/all 01-mismatch hits to FILE [null] -C INT max number of hits to output. >512 for all 01 hits. [250] -s INT seed for random number generator [random] -W disable Smith-Waterman alignment -t trim all reads (usually not recommended) -c match in the colorspace Anyone knows that whether maq 0.7.1 has -N options working or do I have start using maq 0.6.8? Thanks.

10-21-2011, 04:14 AM	#2
pengchy Senior Member Location: China Join Date: Feb 2009 Posts: 116	I wonder how -e will influence the results? How much should I set for the 100pe reads.