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Forum: Bioinformatics 09-16-2011, 12:44 AM
Replies: 0
Views: 2,835
Posted By corthay
SOAPdenovo correction module.

Hi all,

I have a question about the parameters of SOAPdenovo correction module.
I would like to specify the maximum number of kmer frequence cut off. I've checked the usage of corrector and I...
Forum: Bioinformatics 07-29-2011, 12:36 AM
Replies: 35
Views: 12,929
Posted By corthay
Hi all, Finally, allpaths-lg works on my...

Hi all,

Finally, allpaths-lg works on my machine.

My OS is CentOS 5.3 and the version of allpaths-lg is 38003.

I would like to recommend retrying allpaths-lg as it's getting familiar.
Forum: Bioinformatics 02-02-2011, 06:52 PM
Replies: 278
Views: 118,375
Posted By corthay
Hi seb567, Thank you for the detailed...

Hi seb567,

Thank you for the detailed answer.
I am looking forward to the new version:)
Also, it would make me happy if Ray can handle more large kmer
though it might not be important for Ray....
Forum: Bioinformatics 02-01-2011, 08:45 PM
Replies: 278
Views: 118,375
Posted By corthay
Sanger reads

Hi seb567,

I have two questions.

1) Can Ray handle sanger reads such as WGS, Fosmid end ?

2) Does Ray do scaffolding ? The results did not contain N even though
I used paired end as...
Forum: Bioinformatics 01-27-2011, 03:54 PM
Replies: 252
Views: 108,013
Posted By corthay
Hi boetsie, Thanks for your quick reply. I...

Hi boetsie,

Thanks for your quick reply. I understood how uniqueness is guaranteed.
Then, I have two more questions please.

Firstly, I am wondering why the total bases of scaffolds without N...
Forum: Bioinformatics 01-19-2011, 12:49 AM
Replies: 252
Views: 108,013
Posted By corthay
Hi boetsie again, I would like to ask you if...

Hi boetsie again,

I would like to ask you if only unique mapped reads are used for the scaffolding.

If not, I am planing to mask repeat sequence before scaffolding.

Thanks,
Corthay
Forum: Bioinformatics 01-16-2011, 04:48 PM
Replies: 252
Views: 108,013
Posted By corthay
Hi Boetsie, Thanks for the response. ...

Hi Boetsie,

Thanks for the response.

I've just specified "k=2" as clone coverage of BAC ends is almost 5x.
As a result, scaffolds N50 is a bit improved and the number of scaffolds is...
Forum: Bioinformatics 01-12-2011, 04:02 PM
Replies: 252
Views: 108,013
Posted By corthay
BAC / Fosmid end

Hi boetsie,

Can I use additional BAC/Fosmid ends for scaffolding the pre-assebmled contigs
or scaffolds with SSPACE? If it's possible, is there any parameter for this purpose?

Thanks,...
Forum: Bioinformatics 11-11-2010, 03:25 AM
Replies: 19
Views: 29,420
Posted By corthay
Thanks for the idea. I just would like to check...

Thanks for the idea. I just would like to check if deduping is necessary for assembly as Panda Genome paper did it for long insert-sizes libraries.

Corthay
Forum: Bioinformatics 11-09-2010, 11:06 PM
Replies: 19
Views: 29,420
Posted By corthay
Removing duplicates before mapping.

Hi,

Is there any software that removes duplicate of PE or MP read
before mapping ? I would like to remove duplicate before doing
de novo assembly.
Thanks.

Corthay
Forum: Bioinformatics 09-11-2010, 01:29 AM
Replies: 292
Views: 161,570
Posted By corthay
Hi, I got the following strange pileup...

Hi,

I got the following strange pileup results and I am at a loss what to do.
My data is RNA-SEQ and sam file was generated by using Tophat ( ver1.0.14 )
Is there anyone who had similar result...
Forum: Bioinformatics 07-04-2010, 06:58 PM
Replies: 35
Views: 12,929
Posted By corthay
Hi Himalaya, I got the error message when...

Hi Himalaya,

I got the error message when I've used Allpaths ver3.2 so I've used
ver 3-33800 for import my data. Unfortunately, I've not solved the
problem as it may be time-consuming to check...
Forum: Bioinformatics 06-30-2010, 03:29 PM
Replies: 35
Views: 12,929
Posted By corthay
Hi Himalaya, You can use only following...

Hi Himalaya,

You can use only following values for K-mer, as I've roughly checked the source code.
12,20,26,40,64,80,88,96

The "Metric "SEP" is undefined" error is occured when you do not...
Forum: Bioinformatics 06-29-2010, 07:49 PM
Replies: 35
Views: 12,929
Posted By corthay
Hi Himalaya, The file...

Hi Himalaya,

The file "frag_reads_orig.fastb" is a binary sequence
file as input for allpaths. It's generated in import step.

I've used following command for import and standard.
-----...
Forum: Bioinformatics 06-28-2010, 03:47 PM
Replies: 35
Views: 12,929
Posted By corthay
Hi Himalaya, I've used ver. 3-33800 for...

Hi Himalaya,

I've used ver. 3-33800 for import as ver 3.2 have not worked and
I've used ver. 3.2 (stable version) for standard as ver 3-33800 have not worked.
You can get latest source code from...
Forum: Bioinformatics 06-01-2010, 03:08 AM
Replies: 35
Views: 12,929
Posted By corthay
Hi, I have similar problem with allpaths....

Hi,

I have similar problem with allpaths. I've compiled Allpath ver3.2
with following command.

%autoconf
%./configure CC=gcc44 CXX=g++44
%make

It looks successesful but I got...
Forum: Bioinformatics 05-20-2010, 03:51 PM
Replies: 514
Views: 225,331
Posted By corthay
Hi Ben, I appreciate your quick response. ...

Hi Ben,

I appreciate your quick response.
I think I understood it.

Thanks,
Corthay
Forum: Bioinformatics 05-20-2010, 12:27 AM
Replies: 514
Views: 225,331
Posted By corthay
Question Question abou "-n" option.

Hi,

I would like to ask about "-n" option. I would like to map read
following conditions.
1. first N bases must be perfect match.
2. reported position must be 'best' hit.

I used " -n 0 -l...
Forum: Bioinformatics 04-21-2010, 02:04 AM
Replies: 0
Views: 1,870
Posted By corthay
Question about BWA options

Hi,

I've used bwa for 35bp solexa read with following option
"-n 20 -l 15 -k 0 -t 12"
to get reads having perfect match at the first 15bp. And then
I generated .sam file by using "bwa samse"...
Forum: Bioinformatics 04-16-2010, 01:35 AM
Replies: 1
Views: 2,047
Posted By corthay
Reproducibility of CLC de novo assembler

Hi,

I've used CLC de novo assembly to assemble 454 data but
I coundn't get reproducible result as the results are always
a bit different. I would like to know the reason why the
assembler...
Forum: Bioinformatics 03-01-2010, 11:55 PM
Replies: 3
Views: 2,381
Posted By corthay
I've used a script "convert-solexa-to-v2.pl" in...

I've used a script "convert-solexa-to-v2.pl" in wgs-assembler (ver 6.0b) package. Remember quality values are encoded in ASCII by adding 48 (ASCII zero) to the quality value in frg format.
Forum: Bioinformatics 06-05-2009, 02:31 AM
Replies: 292
Views: 161,570
Posted By corthay
I appreciate that you immediately replied to my...

I appreciate that you immediately replied to my question.
I would like to handle the sam format files.
Forum: Bioinformatics 06-04-2009, 10:36 PM
Replies: 292
Views: 161,570
Posted By corthay
Thank you for your speedy response. I have...

Thank you for your speedy response.

I have one more question. I got following results by using bwa(0.4.9), my favorite.
seq-name#0 69 * 0 0 * * 0 0 (sequence) (quality)
seq-name#0 133 * 0 0 *...
Forum: Bioinformatics 06-03-2009, 12:10 AM
Replies: 292
Views: 161,570
Posted By corthay
I would like to generate bam file from blast...

I would like to generate bam file from blast result of EST.

Firstly, I made sam file from blast result using blsat2sam.pl in samtools packages.
Secondly, I have tried to convert from sam file...
Forum: Bioinformatics 01-05-2009, 04:29 PM
Replies: 292
Views: 161,570
Posted By corthay
I downloaded samtools-0.1.1 but could not find...

I downloaded samtools-0.1.1 but could not find "wgsim" or "wgsim_eval.pl" programs which are noted in bwa-0.3.0 documentation.
How can I get these programs ?
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