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Forum: Illumina/Solexa 08-02-2012, 01:55 PM
Replies: 83
Views: 29,115
Posted By ians
awesome! Let us know when you get a look at...

awesome!
Let us know when you get a look at your first 2x250 run!
Forum: Bioinformatics 07-19-2012, 07:47 AM
Replies: 3
Views: 2,522
Posted By ians
454 may be a better platform if you need more...

454 may be a better platform if you need more bases.

it will be difficult to de novo assemble all your amplicons given that they are very similar. For the ones you do know, you could align reads...
Forum: Bioinformatics 07-13-2012, 07:50 AM
Replies: 16
Views: 7,844
Posted By ians
Is there a way to explicitly "keep multithreaded...

Is there a way to explicitly "keep multithreaded alignments in order"?

Don't give up on multithreading. If you can reserve a box, where you don't have to compete for cpu, you may find the run...
Forum: Bioinformatics 07-13-2012, 07:47 AM
Replies: 24
Views: 14,889
Posted By ians
For me it was pretty systematic. My solution...

For me it was pretty systematic.

My solution seems to work thus far as I have rerun 3 samples that previously failed.

I think the problem may stem from when Cufflinks' threads are competing at...
Forum: The Pipeline 07-12-2012, 11:27 AM
Replies: 104
Views: 147,799
Posted By ians
So has that lambda data been released yet??

So has that lambda data been released yet??
Forum: De novo discovery 07-10-2012, 09:57 AM
Replies: 36
Views: 24,844
Posted By ians
Yeah the documentation is a bit rough. This...

Yeah the documentation is a bit rough. This manual (https://wiki.umiacs.umd.edu/cbcb/images/9/99/SOAPdenovo-V1.05.manual.txt) is a bit better.

You're doing a fungus right? How much sequence...
Forum: De novo discovery 07-10-2012, 08:36 AM
Replies: 36
Views: 24,844
Posted By ians
Yes, exactly, Long Insert Mate Pair. Some people...

Yes, exactly, Long Insert Mate Pair. Some people refer to this library type as "Jumping Pairs" as well. LIMP libraries are made through fragment circularization. Otherwise, end sequencing on a...
Forum: De novo discovery 07-10-2012, 07:51 AM
Replies: 36
Views: 24,844
Posted By ians
i'm curious, how are you exporting 454 LIMPs to...

i'm curious, how are you exporting 454 LIMPs to be compatible with SOAP.
We had trouble converting to "Illumina style" LIMPS.
Forum: Bioinformatics 07-09-2012, 09:24 AM
Replies: 2
Views: 1,780
Posted By ians
I suspect you are feeding velvet the reads...

I suspect you are feeding velvet the reads properly; Velvet expects that pairs be in the same file and in forward-reverse order. It's a good idea to read the velvet manual...
Forum: Bioinformatics 07-09-2012, 09:11 AM
Replies: 16
Views: 7,844
Posted By ians
I've seen the "too many open files" error when...

I've seen the "too many open files" error when dealing with alignments else where. I've seen this when sorting very large bam files. This ultimately happens when samtools tries merging all the...
Forum: Bioinformatics 07-09-2012, 09:03 AM
Replies: 24
Views: 14,889
Posted By ians
Solved?

I ran a test run over the weekend using data that had failed before. The run was successful over the weekend!
I ran with just as many threads as the box has. This contrasts with the pervious failed...
Forum: Bioinformatics 07-06-2012, 02:19 PM
Replies: 4
Views: 1,618
Posted By ians
For SNP calling, there's not really much reason...

For SNP calling, there's not really much reason to go past 50bp in length. Especially when comparing to 2x150 bp reads, you'll theoretically have 6x more sampling per basepair with the smaller single...
Forum: Bioinformatics 07-06-2012, 09:46 AM
Replies: 24
Views: 14,889
Posted By ians
I'm still digging through source hoping for some...

I'm still digging through source hoping for some light. Any insight would be strongly appreciated.
Forum: Bioinformatics 07-03-2012, 11:02 AM
Replies: 24
Views: 14,889
Posted By ians
I found the segment_juncs command that died in...

I found the segment_juncs command that died in runs.log.
I tried rerunning the exact command, but with p=1 (singlethreaded), and get the same error.

I've dug through the source of reads.cpp to...
Forum: Bioinformatics 07-03-2012, 09:57 AM
Replies: 24
Views: 14,889
Posted By ians
I am getting the same error with tophat 2.0.0. ...

I am getting the same error with tophat 2.0.0.

tophat.log:
....
[2012-06-30 11:50:15] Mapping right_kept_reads.m2g_um_seg4 against mm9.fa with Bowtie2 (4/4)...
Forum: De novo discovery 06-15-2012, 08:42 AM
Replies: 36
Views: 24,844
Posted By ians
That's pretty dope. I definitely need to try...

That's pretty dope. I definitely need to try this.


I'm curious, did you choose 400bp because you didn't sequence with FLX+? I would think that larger frags would be advantageous.


Yeah, in...
Forum: De novo discovery 06-13-2012, 03:32 PM
Replies: 36
Views: 24,844
Posted By ians
I'm not certain whether that is true or not, but...

I'm not certain whether that is true or not, but here's my thought process: Indeed, SOAP doesnt know explicitly (unless you resolve repeats with reads), however, given the nature of the graph built,...
Forum: De novo discovery 06-13-2012, 09:36 AM
Replies: 36
Views: 24,844
Posted By ians
Yes. We used them as input reads. This...

Yes.


We used them as input reads. This serves as a sort of prescaffolding.


both


-d and -D was set to 0 and 1, so the de bruijn keeps all kmers and all edges.
Forum: Illumina/Solexa 06-05-2012, 07:57 AM
Replies: 83
Views: 29,115
Posted By ians
I mainly had assemblers in mind, where kmer...

I mainly had assemblers in mind, where kmer length is king.
Forum: Illumina/Solexa 06-04-2012, 09:18 AM
Replies: 83
Views: 29,115
Posted By ians
Assume good quality bases, i'd expect Roche to be...

Assume good quality bases, i'd expect Roche to be very nervous with these lengths, especially when sloptigs are made.

Although these read sizes are awesome, there may be quite a lag in analysis...
Forum: Bioinformatics 06-04-2012, 08:46 AM
Replies: 17
Views: 10,696
Posted By ians
It is a good idea (computationally) to reduce...

It is a good idea (computationally) to reduce sequence to only as much sampling as you really need. Which organism did you sequence?


The authors say, I don't have any numbers to share for...
Forum: Bioinformatics 06-04-2012, 07:54 AM
Replies: 17
Views: 10,696
Posted By ians
Be careful here. Most assemblers do not look at...

Be careful here. Most assemblers do not look at header information to establish pairs. Rather, the 1st read in file a is paired with the 1st read in file b. If you remove any reads, be sure you also...
Forum: De novo discovery 05-30-2012, 07:37 AM
Replies: 9
Views: 3,464
Posted By ians
I've been looking for more memory as well. As...

I've been looking for more memory as well.
As far as pre installed software, you could always boot an image of biolinux.
Forum: Bioinformatics 05-30-2012, 07:31 AM
Replies: 4
Views: 1,811
Posted By ians
try gffread...

try gffread (http://cufflinks.cbcb.umd.edu/gff.html)
Forum: Bioinformatics 05-30-2012, 07:26 AM
Replies: 4
Views: 1,719
Posted By ians
Poni, Likely the issue isn't that it is...

Poni,

Likely the issue isn't that it is diploid, but rather you just have a much more complex organism (which is often the case of diploid organisms.) The assembler doesn't really care as it will...
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