SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 63
Search took 0.00 seconds.
Search: Posts Made By: lletourn
Forum: Pacific Biosciences 09-14-2012, 10:31 AM
Replies: 31
Views: 12,433
Posted By lletourn
I finally read quite a bit on that. And...

I finally read quite a bit on that. And conclusion, as they mention on the RunCA page, it depends on your hardware.

The 3 worst steps are 0-overlaptrim-overlap, 1-overlapper and runPartition

If...
Forum: Pacific Biosciences 07-05-2012, 04:38 AM
Replies: 31
Views: 12,433
Posted By lletourn
Look at the 'Building from Source ' section You...

Look at the 'Building from Source ' section
You need to change in AS_global.h
#define AS_READ_MAX_NORMAL_LEN_BITS 11

to something higher.

There is a precompiled binary called wgs7.0-pacbio but...
Forum: Pacific Biosciences 07-05-2012, 04:15 AM
Replies: 31
Views: 12,433
Posted By lletourn
I was able to lower the time to about ~24hours ...

I was able to lower the time to about ~24hours
1- I only use 50x of illumina or ccs reads
2- I modified the .spec file a bit. We have large memeory machines so I changed settings to load as much as...
Forum: Pacific Biosciences 05-26-2012, 05:02 AM
Replies: 31
Views: 12,433
Posted By lletourn
I just noticed, why the stopAfter=Overlaper? ...

I just noticed, why the stopAfter=Overlaper?

Did they tell you to run something manually?
Forum: Pacific Biosciences 05-25-2012, 11:50 AM
Replies: 31
Views: 12,433
Posted By lletourn
Of course! I am really looking forward to running...

Of course! I am really looking forward to running this this weekend.
Forum: Pacific Biosciences 05-25-2012, 10:42 AM
Replies: 31
Views: 12,433
Posted By lletourn
Yes, yes please do!

Yes, yes please do!
Forum: Pacific Biosciences 05-25-2012, 06:11 AM
Replies: 31
Views: 12,433
Posted By lletourn
We will be upgrading our smart portal from 1.3.0...

We will be upgrading our smart portal from 1.3.0 to 1.3.1 soon (in a few days) but I would really like to have pacbioToCa work in a reasonable amount of time for 2 reasons

1- Many people that do...
Forum: Pacific Biosciences 05-24-2012, 04:50 PM
Replies: 31
Views: 12,433
Posted By lletourn
I'm also running into speed issues. My 50x...

I'm also running into speed issues. My 50x coverage was estimated to take 4weeks to complete.

I would be surprised if all the people using it are ready to wait that long :-)
Forum: Bioinformatics 10-28-2011, 10:50 AM
Replies: 278
Views: 94,752
Posted By lletourn
about mates, do we need to revcomp the illumina...

about mates, do we need to revcomp the illumina reads to keep them as innies, or Ray doesn't care if they're outties or innies?
Forum: Bioinformatics 10-25-2011, 10:06 AM
Replies: 8
Views: 9,111
Posted By lletourn
I read the first post too fast. At our center we...

I read the first post too fast. At our center we use unaligned bams as inputs to bwa using the technique I mentioned above. This works with paired and single datasets.

What I propose is fine for...
Forum: Bioinformatics 10-25-2011, 05:23 AM
Replies: 8
Views: 9,111
Posted By lletourn
according to the bwa manual page: ...

according to the bwa manual page:
http://bio-bwa.sourceforge.net/bwa.shtml

-b Specify the input read sequence file is the BAM format. For paired-end data, two ends in a pair must be grouped...
Forum: Bioinformatics 10-06-2011, 08:14 AM
Replies: 12
Views: 3,511
Posted By lletourn
You're right, look only at the exomes+UTR. ...

You're right, look only at the exomes+UTR.

Or give it any interval and also give it a refGene formatted file (the geneList option only work if you also pass an interval. I think that's a bug).
Forum: Bioinformatics 10-05-2011, 06:20 PM
Replies: 12
Views: 3,511
Posted By lletourn
Yes, GATK is pretty Finicky about the RG tag and...

Yes, GATK is pretty Finicky about the RG tag and karyotypic order of chromosomes (GATK doesn't like chr1, chr10, chr11, it likes chr1, chr2, chr3, etc).

You could use Picards AddOrReplaceReadGroup...
Forum: Bioinformatics 10-04-2011, 03:03 PM
Replies: 12
Views: 3,511
Posted By lletourn
Yes but it's a gross approximation. You lose the...

Yes but it's a gross approximation. You lose the reads that are trimmed/clipped. the ones that don't align, the ones not on target the bases with too low quality, the reads that have a too-low...
Forum: Bioinformatics 10-03-2011, 07:58 AM
Replies: 278
Views: 94,752
Posted By lletourn
Thumbs up Wow impressive numbers. I think I'll try 1.7...

Wow impressive numbers.

I think I'll try 1.7 on some of my "old" assemblies to see the difference.
Forum: Bioinformatics 10-03-2011, 07:36 AM
Replies: 278
Views: 94,752
Posted By lletourn
Great work Seb! Did you run 1.7 on the...

Great work Seb!

Did you run 1.7 on the parrot data (Assemblathon 2) to compare with Ray 1.6.1?
Forum: Bioinformatics 09-27-2011, 07:34 AM
Replies: 12
Views: 3,511
Posted By lletourn
As with Heisman I prefer DepthOfCoverage...

As with Heisman I prefer DepthOfCoverage especially for exomes because of the percent reads at X depth feature.

For you interval list it can tell you which percentage of your bases are higher than...
Forum: Bioinformatics 09-27-2011, 07:29 AM
Replies: 1
Views: 4,823
Posted By lletourn
We had the same issue at the beggining, hitting...

We had the same issue at the beggining, hitting >60% dupes. We had to start with more dna and use a bit bigger fragment lengths to lower the values. We now typically get 20-30% dups.

Lets not...
Forum: Bioinformatics 08-13-2011, 06:51 AM
Replies: 2
Views: 5,357
Posted By lletourn
I finally found my answer. By default GATK...

I finally found my answer.

By default GATK downsamples by sample. The downsampling coverage is...drum roll...1000.

To fix this set the number of bins *AND* set -dt NONE

Why one would...
Forum: Bioinformatics 08-13-2011, 06:31 AM
Replies: 2
Views: 5,357
Posted By lletourn
GATK DepthOfCoverage at high depth

I have a sample on which custom capture was done. Many of the baits have >2000x coverage.

When running DepthOfCoverage initially I never saw values >500x but then noticed I forgot to set the bins...
Forum: De novo discovery 08-09-2011, 06:43 AM
Replies: 82
Views: 42,829
Posted By lletourn
I wanted to add parameters to allow for -long or...

I wanted to add parameters to allow for -long or not. Right now the script assumes -long is passed (in 4 of our experimets we added 454 RNA-Seq reads to the mix).

I'll fix this and post the...
Forum: De novo discovery 08-09-2011, 04:36 AM
Replies: 82
Views: 42,829
Posted By lletourn
Yeah I know, I computed RPKM separately. I...

Yeah I know, I computed RPKM separately. I mis-phrased what I meant.
I should go back and edit.
Thanks.
Forum: De novo discovery 08-08-2011, 06:41 PM
Replies: 82
Views: 42,829
Posted By lletourn
I'm also really interested in the opinions of...

I'm also really interested in the opinions of others on this topic.

I've used the make 1 assembly (with velvet-oases) annotate and compare RPKMs from the assembly it seems to work well for...
Forum: Illumina/Solexa 08-04-2011, 08:14 AM
Replies: 2
Views: 3,416
Posted By lletourn
I actually asked tech support about this, here is...

I actually asked tech support about this, here is their answer:
Forum: Bioinformatics 06-17-2011, 07:28 AM
Replies: 1
Views: 1,923
Posted By lletourn
I solved that problem in january after 2 weeks of...

I solved that problem in january after 2 weeks of thinking our nfs server was collapsing. One email to tech support fixed it.

I would have liked for them to acknowledge the problem and notify...
Showing results 1 to 25 of 63

 


All times are GMT -8. The time now is 10:04 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO