Forum: Bioinformatics
09-16-2011, 12:44 AM
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Replies: 0
Views: 2,835
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...
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Forum: Bioinformatics
07-29-2011, 12:36 AM
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Replies: 35
Views: 12,929
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.
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Forum: Bioinformatics
02-02-2011, 06:52 PM
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Replies: 278
Views: 118,375
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....
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Forum: Bioinformatics
02-01-2011, 08:45 PM
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Replies: 278
Views: 118,375
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...
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Forum: Bioinformatics
01-27-2011, 03:54 PM
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Replies: 252
Views: 108,013
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...
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Forum: Bioinformatics
01-19-2011, 12:49 AM
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Replies: 252
Views: 108,013
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Forum: Bioinformatics
01-16-2011, 04:48 PM
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Replies: 252
Views: 108,013
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...
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Forum: Bioinformatics
01-12-2011, 04:02 PM
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Replies: 252
Views: 108,013
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,...
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Forum: Bioinformatics
11-11-2010, 03:25 AM
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Replies: 19
Views: 29,420
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Forum: Bioinformatics
11-09-2010, 11:06 PM
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Replies: 19
Views: 29,420
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
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Forum: Bioinformatics
09-11-2010, 01:29 AM
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Replies: 292
Views: 161,570
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...
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Forum: Bioinformatics
07-04-2010, 06:58 PM
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Replies: 35
Views: 12,929
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...
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Forum: Bioinformatics
06-30-2010, 03:29 PM
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Replies: 35
Views: 12,929
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...
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Forum: Bioinformatics
06-29-2010, 07:49 PM
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Replies: 35
Views: 12,929
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.
-----...
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Forum: Bioinformatics
06-28-2010, 03:47 PM
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Replies: 35
Views: 12,929
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...
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Forum: Bioinformatics
06-01-2010, 03:08 AM
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Replies: 35
Views: 12,929
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...
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Forum: Bioinformatics
05-20-2010, 03:51 PM
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Replies: 514
Views: 225,331
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Forum: Bioinformatics
05-20-2010, 12:27 AM
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Replies: 514
Views: 225,331
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...
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Forum: Bioinformatics
04-21-2010, 02:04 AM
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Replies: 0
Views: 1,870
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"...
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Forum: Bioinformatics
04-16-2010, 01:35 AM
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Replies: 1
Views: 2,047
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...
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Forum: Bioinformatics
03-01-2010, 11:55 PM
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Replies: 3
Views: 2,381
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Forum: Bioinformatics
06-05-2009, 02:31 AM
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Replies: 292
Views: 161,570
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Forum: Bioinformatics
06-04-2009, 10:36 PM
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Replies: 292
Views: 161,570
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 *...
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Forum: Bioinformatics
06-03-2009, 12:10 AM
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Replies: 292
Views: 161,570
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...
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Forum: Bioinformatics
01-05-2009, 04:29 PM
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Replies: 292
Views: 161,570
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