SOAP2 -v doesn't work

[zhongj]

I have the same problem，have anyone figured it out? pls let me know.Thanks!

[Insane]

Hello everybody,

Does anybody knows how to deal with that problem?
I would like to work with 4 mismatches per read and I don't know how to do...

[karthikprabu]

I would like to know

[sediener]

Sorry I can't help more, a co-worker told me of that difference btw SOAP and SOAP2 so that's about all I know. I'll ask him later today to see if he's figured out more of the rules.

It would be nice if there was a better standard for documentation of Bioinformatics apps. Seems like the only way to use some of these programs correctly is to contact the author.

[baohua100]

-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
0: exact match only
1: 1 mismatch match only
2: 2 mismatch match only
4: find the best hits

what‘ that mean？ If i want to find alignment with 3 mismatch, how to set the parameter M?

[sediener]

You have to use it with some combination of -M # . I'm not sure why but that's what I've been told.

- Steve

[baohua100]

SOAP2 -v maximum number of mismatches allowed on a read

I have tried -v 3 -v 2 -v 4 for 50bp read, but the maximum number of mismatch in the output is always 2. there are no read wish mismatch 3 or more.



my command:
soap -a reads/PT0012.3_1.fastq -b reads/PT0012.3_2.fastq -D genome.fa.index -m 0 -x 500000 -u 3.unmap -o 3.paired -2 3.unpaired -v 3 -r 2 -p 2




Usage: soap [options]
-a <str> query a file, *.fq, *.fa
-b <str> query b file
-D <str> reference sequences indexing table, *.index format
-o <str> output alignment file(txt)
-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
0: exact match only
1: 1 mismatch match only
2: 2 mismatch match only
4: find the best hits
-u <str> output unmapped reads file
-t output reads id instead reads name, [none]
-l <int> align the initial n bps as a seed [256] means whole length of read
-n <int> filter low-quality reads containing >n Ns before alignment, [5]
-r [0,1,2] how to report repeat hits, 0=none; 1=random one; 2=all, [1]
-m <int> minimal insert size allowed, [400]
-x <int> maximal insert size allowed, [600]
-2 <str> output file of unpaired alignment hits
-v <int> maximum number of mismatches allowed on a read. [5] bp
-s <int> minimal alignment length (for soft clip) [255] bp
-g <int> one continuous gap size allowed on a read. [0] bp
-R for long insert size of pair end reads RF. [none](means FR pair)
-e <int> will not allow gap exist inside n-bp edge of a read, default=5
-p <int> number of processors to use, [1]

-h this help