Bwbble Alignment Program

[lwhitmore]

Does any one know how to implement the options in the bwbble allignment program? I can't seem to get it correct

Here are some commands i have tried
bwbble align -M 29Family_L1MdA_I_LW.fa SRR519779test_LW.fastq
bwbble align M 29Family_L1MdA_I_LW.fa SRR519779test_LW.fastq
bwbble align 29Family_L1MdA_I_LW.fa SRR519779test_LW.fastq M
bwbble align 29Family_L1MdA_I_LW.fa SRR519779test_LW.fastq -n 5

Thanks for anyone who can help

Leanne

[mastal]

the usage is:

bwbble align [options] seq_fasta reads_fastq [output_aln]

so one of your first two attempts above should work, but I'm guessing that if you use M as an option, you need to specify a value for the mismatch penalty M.

[lwhitmore]

It keeps saying that I need a bwt file whenever I put an option in

[mastal]

Presumably that is the genome index file, sounds like it isn't recognising your syntax.

Have you created a genome index before trying to run an alignment?

see

http://viq854.github.com/bwbble

[lwhitmore]

Yes I am currently getting an error when I try and index my genome

[lwhitmore]

Here is the error i get

**** BWT Index ****
Done reading a sequence of size 6565 from FASTA
Done reading FASTA file. Total sequence length read = 6565
SAIS time: 0.00 sec
BWT compression time: 0.00 sec
C-array construction time: 0.00 sec
O-array construction time: 0.00 sec
Total BWT construction time: 0.00 sec
bwbble(2289) malloc: *** error for object 0x1a000000000000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap

[lwhitmore]

So even with the error above the program still seems to be able to align to the indexes generated

also I cant seem to get the mismatch option to work when I sent -n to 3 it still only allows 1 mismatch

Ive also tried setting -M 1 and it still doesn't appear to allow more than one mismatch

Again any helpful would be most appreciated
Thanks Leanne

[mastal]

Having a quick look through the code (module align.c), the default
parameters appear to be:

void set_default_aln_params(aln_params_t* params) {
params->gape_score = 4;
params->gapo_score = 11;
params->mm_score = 3;
params->max_diff = 0;
params->max_gape = 6;
params->max_gapo = 1;
params->seed_length = 32;
params->max_diff_seed = 2;
params->max_entries = 3000000;
params->use_precalc = 0;
params->matched_Ncontig = 0;
params->is_multiref = 1;
params->max_best = 30;
params->no_indel_length = 5;
params->n_threads = 1;
}

I think you will have to email the program's authors for more help.

[lwhitmore]

Ok thanks for your help!