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seb567 · 01-13-2014, 06:52 AM

Originally posted by bossanova352 View Post

I'm trying to use Ray on some environmental metagenomes, but every time I set up a run, the output contig and scaffold files are empty. I haven't seen any indication during the assembly run, and all sequences are recognized by Ray. One possibility that comes to mind is from some errors that came up while compiling. Specifically, when trying to use the make install command, an error pops up saying there is no README file in ray-build/RayPlatform. If I place the README file in RayPlatform and try again, I get an error saying there is already a file named RayPlatform.

Edit: After reinstalling Ray with the developer package, there are no installation errors. As of now, I'm stumped why there are no assembled sequences in either of the output Contigs.fasta or Scaffolds.fasta files.

What is the content of RayOutput/NumberOfSequences.txt ?

Do you have any error in your standard output file ? ("grep Error log.stdout")

VidJa · 01-13-2014, 06:14 AM

I'm trying to use Ray with a mix of Illumina SE and 454 data using the -amos
mpiexec -n 10 Ray -s illumina.fasta -s 454.fasta -k 31 -amos -o mix
454 reads have an avg length of 396bp and the illumina reads are 60bp

The resulting amos file AMOS.afg can be browsed using Tablet, but I noticed that the original read names are converted to just a number and thus making it impossible to easily trace which reads end up in a particular contig. Is it possible to save the original readnames in the AMOS output?

bossanova352 · 01-11-2014, 10:49 AM

I'm trying to use Ray on some environmental metagenomes, but every time I set up a run, the output contig and scaffold files are empty. I haven't seen any indication during the assembly run, and all sequences are recognized by Ray. One possibility that comes to mind is from some errors that came up while compiling. Specifically, when trying to use the make install command, an error pops up saying there is no README file in ray-build/RayPlatform. If I place the README file in RayPlatform and try again, I get an error saying there is already a file named RayPlatform.

Edit: After reinstalling Ray with the developer package, there are no installation errors. As of now, I'm stumped why there are no assembled sequences in either of the output Contigs.fasta or Scaffolds.fasta files.

seb567 · 11-21-2013, 07:34 AM

Originally posted by Brian E View Post

So, to add to an already massive thread, it's looking like Ray is going to be the assembler we're going to be using for our Metagenome work,

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

Ray Meta: scalable de novo metagenome assembly and profiling - SEQanswers

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

Discussion of any scientific study related to high content or next generation genomics. Whole genome association, metagenomics, digital gene expression, etc.

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

Originally posted by Brian E View Post

and I was wondering if it is possible to obtain the location that each read ends up in the assembly.

There is the -amos option, but on the mailing list, I see more people relying on post-assembly read mapping onto the contigs.

Originally posted by Brian E View Post

We're using multiple biological replicates, sequenced separately (multiplexed) and we know that there is some variation in the abundance of the organisms that are present in the community. What I would like is the contribution of each individual sample to the local coverage of the whole assembly. I think this could help with pulling out individual genomes.

If you are sequencing barcoded samples, then demultiplexing should be done before feeding the data to Ray.

Originally posted by Brian E View Post

I know could get at this by mapping with e.g. Bowtie, but if it is possible to keep track of where these reads are ending up, it would save a significant amount of time on our computer cluster allocation. Is this possible?

As stated above, Ray can generate an AMOS file, which contains read usage.

Séb

Brian E · 11-20-2013, 02:48 PM

So, to add to an already massive thread, it's looking like Ray is going to be the assembler we're going to be using for our Metagenome work, and I was wondering if it is possible to obtain the location that each read ends up in the assembly. We're using multiple biological replicates, sequenced separately (multiplexed) and we know that there is some variation in the abundance of the organisms that are present in the community. What I would like is the contribution of each individual sample to the local coverage of the whole assembly. I think this could help with pulling out individual genomes.
I know could get at this by mapping with e.g. Bowtie, but if it is possible to keep track of where these reads are ending up, it would save a significant amount of time on our computer cluster allocation. Is this possible?

seb567 · 08-12-2013, 08:46 AM