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Forum: Introductions 01-29-2019, 11:45 AM
Replies: 2
Views: 1,376
Posted By seb567
According to the documentation...

According to the documentation (https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf), that would be like this:
Forum: Bioinformatics 01-29-2019, 11:39 AM
Replies: 3
Views: 620
Posted By seb567
If you'are using "bwa sampe" for aligning, the...

If you'are using "bwa sampe" for aligning, the documentation (http://bio-bwa.sourceforge.net/bwa.shtml) says:



I don't know if it is the case with "bwa mem" or with "bwa aln".
Forum: De novo discovery 02-02-2018, 06:57 AM
Replies: 2
Views: 2,297
Posted By seb567
This looks like contamination. You are...

This looks like contamination.

You are expecting a 1.65 Mb genome.

The sum of contig length is 2.4 Mb.


When you searched the low-coverage contigs against the NCBI database, did they have...
Forum: Bioinformatics 02-01-2018, 11:36 AM
Replies: 2
Views: 837
Posted By seb567
Thanks for posting the solution.

Thanks for posting the solution.
Forum: Bioinformatics 02-12-2014, 10:56 AM
Replies: 278
Views: 104,073
Posted By seb567
Ray 2.3.1

Hi,

Ray 2.3.1 is now available on http://denovoassembler.sourceforge.net/download.html.

Significant changes:

* This version includes "Surveyor" to compute similarity (or distance) matrices...
Forum: Bioinformatics 01-15-2014, 07:43 AM
Replies: 278
Views: 104,073
Posted By seb567
Short seeds mean that they are not connecting...

Short seeds mean that they are not connecting with one another.

Can you provide a couple of lines from CoverageDistribution.txt (head) ?
Forum: Bioinformatics 01-13-2014, 01:53 PM
Replies: 278
Views: 104,073
Posted By seb567
Each sequence needs to be on one line (this is a...

Each sequence needs to be on one line (this is a current limitation of fasta support in Ray).

That's presumably the issue.
Forum: Bioinformatics 01-13-2014, 01:23 PM
Replies: 278
Views: 104,073
Posted By seb567
Can you paste the 10 first lines of your file...

Can you paste the 10 first lines of your file named SFBloom_paired_trimmed_1.fa ?
Forum: Bioinformatics 01-13-2014, 05:52 AM
Replies: 278
Views: 104,073
Posted By seb567
This is not currently possible because Ray does...

This is not currently possible because Ray does not read or store read names at all.
Forum: Bioinformatics 01-13-2014, 05:52 AM
Replies: 278
Views: 104,073
Posted By seb567
What is the content of...

What is the content of RayOutput/NumberOfSequences.txt ?

Do you have any error in your standard output file ? ("grep Error log.stdout")
Forum: Bioinformatics 11-21-2013, 06:34 AM
Replies: 278
Views: 104,073
Posted By seb567
There is a thread for Ray Meta (Ray for...

There is a thread for Ray Meta (Ray for Metagenomics):

http://seqanswers.com/forums/showthread.php?t=26278

Paper: http://genomebiology.com/2012/13/12/R122



There is the -amos option, but...
Forum: Literature Watch 10-31-2013, 12:40 PM
Replies: 29
Views: 20,637
Posted By seb567
Ray 2.3.0

Hello,

I am proud to announce the immediate availability of Ray 2.3.0 (434 KB).



Most significant change:

- add -detect-sequence-files to detect supported files
Forum: Bioinformatics 10-25-2013, 07:59 AM
Replies: 3
Views: 2,355
Posted By seb567
That's a good idea, but the coverage depth for...

That's a good idea, but the coverage depth for each sample kmers needs to normalized with the number of reads since sample A may have twice the number of reads present in sample B.

Coverage depth...
Forum: Bioinformatics 10-23-2013, 12:46 PM
Replies: 3
Views: 2,355
Posted By seb567
Re: assemble multiple related metagenome samples

Hello,


Why do you want to assemble multiple related metagenome samples together ?

If you look at Cortex ( http://www.nature.com/ng/journal/v44/n2/full/ng.1028.html ),
each vertex in their de...
Forum: Bioinformatics 08-12-2013, 08:46 AM
Replies: 278
Views: 104,073
Posted By seb567
No. The command above is to build Ray with gz...

No. The command above is to build Ray with gz support but no bz2 support.


Did you try:

make clean
make HAVE_LIBZ=y HAVE_LIBBZ2=n
Forum: Bioinformatics 08-11-2013, 10:35 AM
Replies: 278
Views: 104,073
Posted By seb567
The package you installed with yum is...

The package you installed with yum is 2.1.0-6.fc19 (not 2.2.0).


So if you also want 2.2.0, can you try this (with gz support but without bz2 support):


make clean
make HAVE_LIBZ=y...
Forum: Bioinformatics 08-11-2013, 10:24 AM
Replies: 278
Views: 104,073
Posted By seb567
You can simply type this to install in Fedora 19:...

You can simply type this to install in Fedora 19:

sudo yum install Ray-openmpi




For your buddy libbz2.so, can you type this command:

file -L /usr/lib64/libbz2.so
Forum: Bioinformatics 08-11-2013, 10:09 AM
Replies: 278
Views: 104,073
Posted By seb567
Did you try to build Ray using the Makefile using...

Did you try to build Ray using the Makefile using the
"make" command ?


Which version of Ray are you building ?


In Fedora 19, there is the precompiled package Ray-openmpi.x86_64
that...
Forum: Bioinformatics 08-11-2013, 09:35 AM
Replies: 278
Views: 104,073
Posted By seb567
Hello, The message "skipping incompatible...

Hello,

The message "skipping incompatible /usr/lib64/libbz2.so when searching for -lbz2"
means something I guess. I never saw this message before.
It is likely related to your tool chain, not...
Forum: Bioinformatics 07-30-2013, 09:29 AM
Replies: 278
Views: 104,073
Posted By seb567
It says "Rank 43 reached 536870000 vertices from...

It says "Rank 43 reached 536870000 vertices from seed 0, flow 2"

That is a lot of vertices !

Which version of Ray are you using ?

I believe that this issue was fixed in Ray 2.2.0. The ticket...
Forum: Bioinformatics 07-30-2013, 09:26 AM
Replies: 278
Views: 104,073
Posted By seb567
How many reads do you have ? This information is...

How many reads do you have ? This information is available in the file

RayOutput/NumberOfSequences.txt


This is usually due to using k-mers that are longer than reads or to assembling 0 reads.
Forum: Bioinformatics 07-30-2013, 09:25 AM
Replies: 278
Views: 104,073
Posted By seb567
Can you provide the output of this command: ...

Can you provide the output of this command:

type mpicxx
Forum: Bioinformatics 07-30-2013, 09:24 AM
Replies: 278
Views: 104,073
Posted By seb567
Hi ! You can use the data in the...

Hi !

You can use the data in the LibraryData.xml to check the actual distribution of your libraries and then maybe show this information to your laboratory technician. The 303 bp reported by Ray...
Forum: Literature Watch 06-12-2013, 09:19 AM
Replies: 29
Views: 20,637
Posted By seb567
The problem is related to your MPI installation....

The problem is related to your MPI installation. It seems that mpiexec wants to use ssh to connect to tll-bioinfo02.

Maybe tll-bioinfo02 is listed in a hostfile and that your MPI installation is...
Forum: Bioinformatics 06-03-2013, 07:00 AM
Replies: 4
Views: 3,440
Posted By seb567
http://www.dwc.knaw.nl/DL/publications/PU00018235....

http://www.dwc.knaw.nl/DL/publications/PU00018235.pdf
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