[kulikov]

Hi Kulikov,

Are the contigs of summary1.txt a mix of the two assemblies? In other words; are parts of the contigs present in other contigs? Because what i think has happened, is that reads could map to multiple contigs. SSPACE does not allow reads to map to multiple contigs.

Boetsie

Hi Boetsie,

No, contigs1 is not a mix. This is just a raw set of contigs. contigs2 are obtained from contigs1 after repeat resolving stage. I guess some parts of contigs may be present in other contigs (in contigs1), but it is still strange that no pair is found on contigs.

Btw, what happens if not only a read, but also its reverse complementary is mapped somewhere?

[boetsie]

Hi Boetsie,

No, contigs1 is not a mix. This is just a raw set of contigs. contigs2 are obtained from contigs1 after repeat resolving stage. I guess some parts of contigs may be present in other contigs (in contigs1), but it is still strange that no pair is found on contigs.

Btw, what happens if not only a read, but also its reverse complementary is mapped somewhere?

Could you check two things;
- are there are any readfiles generated for this project in folder 'reads'?
- If there are, can you try to run it on a subset of your contigs (2 contigs for example) and see how if any reads align.

If a read can map to more than one location (reverse complement and normal) it is not used for scaffolding.

Regards,
Boetsie

[Ashu]

Hi Boetsie,
I was trying to use test the with extension x -1 , and it takes a lot of time and memory, I dont have a memory problem, but time. What is your experience with a mouse genome, around 75x coverage
Thank you in advance,
cheers,
Ashu

[boetsie]

Hi Ashu,

I know it takes a lot of time to extend the contigs, especially with large genomes. Can you tell me what part takes up the most time?

I've speeded up some things of contig extension in the SSPACE premium, you can give it a shot. One thing is the mapping of the reads against the contigs, which is now multithreaded. Another is the search for partial overlap of the reads on the contigs, which uses a faster method.

I've never ran SSPACE extension on a eukaryotic genome myself, sorry i can't tell you.

Regards,
Boetsie

[Ashu]

Hi Boetsie,
Thank you for your suggestions, I will try it. Can you may be show the parameters you used for the panda.
Thank you,
Cheers,
Ashu

[boetsie]

Hi Boetsie,
Thank you for your suggestions, I will try it. Can you may be show the parameters you used for the panda.
Thank you,
Cheers,
Ashu

For the Panda genome I did not do any extension. For scaffolding I used

-x = 0
-k = 3
-a = 0.7
-n = 15

Regards,
Boetsie

[kulikov]

Could you check two things;
- are there are any readfiles generated for this project in folder 'reads'?
- If there are, can you try to run it on a subset of your contigs (2 contigs for example) and see how if any reads align.

If a read can map to more than one location (reverse complement and normal) it is not used for scaffolding.

Regards,
Boetsie

Hi Boetsie,

Yes, this was caused by the fact that each contig was present together with its reverse complementary. After leaving only one contig from each pair everything works great.

Thank you for your help and for designing SSPACE! =)

Best,
Sasha

[boetsie]

Hi Boetsie,

Yes, this was caused by the fact that each contig was present together with its reverse complementary. After leaving only one contig from each pair everything works great.

Thank you for your help and for designing SSPACE! =)

Best,
Sasha

Ah, great! Good that the problem is solved. I already thought something like that was happening.

Thanks for the support and the nice comments!

Boetsie

[colindaven]

Hi Sspace users,

just a bug report and solution we experienced here on a Suse 64 bit system.

We had this error

"
=>Thu Sep 8 13:45:01 2011: Building Bowtie index for contigs (/working/colin/seq/cloneC/sspace/C40A_454AllContigs.fna)

Bowtie-build error; -1 at (directory)"

There was an issue with bowtie-build.

We solved by making sure the bowtie executables were all executable, ie. chmod a+x on the files in the SSPACE/bowtie subdirectory. We also did chmod g+w though that likely didn't do much.

cheers

[rskr]

What is the run-time complexity for SSPACE? It seems that we are having trouble getting it to scale, and what was taking days on a smaller set is now taking several weeks on a larger set. Also is there anyway to get the alignments to be done in parallel?

[boetsie]

What is the run-time complexity for SSPACE? It seems that we are having trouble getting it to scale, and what was taking days on a smaller set is now taking several weeks on a larger set. Also is there anyway to get the alignments to be done in parallel?

Can you comment on what part of SSPACE you are having trouble, is it with contig extension or scaffolding?

In the SSPACE premium version i've made the read-in and Bowtie mapping multithreaded. Also the results are immmediately read-in into SSPACE, instead of writing the results to files and reading of those files. Extension has also speeded-up by immediately read-in of the results and faster way of finding overlap of the reads on the contigs.

Regards,
Boetsie

[rskr]

Can you comment on what part of SSPACE you are having trouble, is it with contig extension or scaffolding?

In the SSPACE premium version i've made the read-in and Bowtie mapping multithreaded. Also the results are immmediately read-in into SSPACE, instead of writing the results to files and reading of those files. Extension has also speeded-up by immediately read-in of the results and faster way of finding overlap of the reads on the contigs.

Regards,
Boetsie

The basic version, but one that I have modified to read bwa files instead.

[Kennels]

Hi boetsie

Is there a version for an Itanium machine (linux IA64)? Or anyway to compile it for such?

cheers,
kennels

[boetsie]

Hi boetsie

Is there a version for an Itanium machine (linux IA64)? Or anyway to compile it for such?

cheers,
kennels

Hi Kennels,

I think the perl script will work everywhere, so it depends on Bowtie.
if there is a bowtie version that works for the Itanium machine, you can place the bowtie scripts in the bowtie folder of SSPACE.

Regards,
Boetsie

[Lisa0508]

Hi Boetzer,
Thank you so much for your quick reply and patient explanation! It's working now. I just got registered on this forum yesterday. All settings were in a default condition. I'm very sorry I did not check the private message option. Now it's O.K. to recieve private messages. Thank you again!
Regards,
Lisa