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Search: Posts Made By: aeonsim
Forum: Vendor Forum 03-08-2015, 04:09 AM
Replies: 108
Views: 49,768
Posted By aeonsim
I'd acctually say they're worse than what we had,...

I'd acctually say they're worse than what we had, considering your using PE80bp and the first 10 or so bases on the forward reads shows an average Quality score drop of ~10 on the Phred Scale (~30 to...
Forum: Vendor Forum 01-13-2015, 03:07 AM
Replies: 108
Views: 49,768
Posted By aeonsim
So I've been getting some initial test data back...

So I've been getting some initial test data back from a Nextseq 500 and I'm really not happy with it compared to the Hiseq.

The data quality from the NextSeq is substantially worse than that from...
Forum: Illumina/Solexa 01-15-2014, 12:47 PM
Replies: 100
Views: 34,939
Posted By aeonsim
At least with Cows there are multiple groups...

At least with Cows there are multiple groups sequencing as many animals as they can afford to get a better understanding of variation within and between breeds. Even with the previous prices the...
Forum: Illumina/Solexa 01-15-2014, 11:08 AM
Replies: 100
Views: 34,939
Posted By aeonsim
Read that, it provides the basic information but...

Read that, it provides the basic information but not much more.

The one really stupid and highly annoying thing about the Hiseq X is the restriction to only sequence Human genomes (at the $1K 30x...
Forum: Illumina/Solexa 01-14-2014, 11:16 AM
Replies: 100
Views: 34,939
Posted By aeonsim
What I'd like is some more detailed explanation...

What I'd like is some more detailed explanation of the 2-dye system the NextSeq 500 is using. I assume they provide C & A tagged with Red, T & A tagged with green & G untagged, thus C should be pure...
Forum: Bioinformatics 10-22-2013, 03:33 PM
Replies: 3
Views: 2,051
Posted By aeonsim
Data is for WGS Bos Taurus, ~3GB Genome, using...

Data is for WGS Bos Taurus, ~3GB Genome, using 101bp PE or 109bp PE PCR-Free Libraries.
Forum: Bioinformatics 10-22-2013, 08:52 AM
Replies: 3
Views: 2,051
Posted By aeonsim
PCR-Free Libraries & Bioinformatic PCR Duplicate detection?

Does any one have any thoughts or experience with regards to the Bioinformatics pipeline for Illumina PCR-Free libraries?

Especially with regards to the need to run Picards MarkDuplicates or some...
Forum: Bioinformatics 07-07-2013, 02:59 PM
Replies: 3
Views: 1,502
Posted By aeonsim
Just remember QUAL score will be confounded by...

Just remember QUAL score will be confounded by Copy Number and SVs present in your individual/population. You'll get some very high QUAL scores for sites in the genome that have higher than expected...
Forum: Bioinformatics 06-19-2013, 12:19 PM
Replies: 1
Views: 1,018
Posted By aeonsim
Working/Visualising Phased VCF files?

Hi can any one recommend any software for working with Phased VCF files?

I've a complete 4 generation pedigree (Grandparents, Parents, Proband, Children) which I've phased using a couple of...
Forum: General 04-07-2013, 11:10 AM
Replies: 1
Views: 1,252
Posted By aeonsim
Use the GATK Callable Loci tool with the mindepth...

Use the GATK Callable Loci tool with the mindepth & maxdepth options set to what you want and get it to output the bed file, read the Docs for details....
Forum: General 04-07-2013, 05:25 AM
Replies: 1
Views: 1,092
Posted By aeonsim
I believe that's normal, it's similar to what we...

I believe that's normal, it's similar to what we usually see when sequencing. I've never pull investigated the cause of it but I suspect it may be due to score differences between Heterozygous and...
Forum: Bioinformatics 03-01-2013, 03:53 PM
Replies: 5
Views: 3,851
Posted By aeonsim
With regards to the two machines I'd suggest the...

With regards to the two machines I'd suggest the second may be the better option, note this is just in general (wrt bioinformatics) as I do not have nor have ever used the Miseq software.

For CPU...
Forum: Bioinformatics 02-04-2013, 10:38 AM
Replies: 2
Views: 3,949
Posted By aeonsim
Not sure what's going on there but there are a...

Not sure what's going on there but there are a number of other filtering tools that I'd recommend over vcf-annotate.

http://snpeff.sourceforge.net/SnpSift.html is very powerful and feature rich...
Forum: Bioinformatics 02-03-2013, 03:50 AM
Replies: 0
Views: 831
Posted By aeonsim
Is picard MarkDuplicates Sample/Readgroup Aware?

As above:

Is Picards MarkDuplicates safe to run on a multisample/multilibrary bam, or will it remove all reads that map to the same position even if they belong to different Samples?

Thanks
Forum: Bioinformatics 11-07-2012, 06:50 AM
Replies: 15
Views: 4,568
Posted By aeonsim
If it's do able the approach described by Simon &...

If it's do able the approach described by Simon & mbblack is definitely worth considering. Especially seeing it can allow you to plug the server into a rack next to the NAS minimizing any network...
Forum: Bioinformatics 11-06-2012, 12:03 PM
Replies: 15
Views: 4,568
Posted By aeonsim
You need to balance RAM and processor power. For...

You need to balance RAM and processor power. For Sequence analysis generally additional CPU cores are more important than a few Hundred more Mhz.

Rough specs for a recommendation would be:
2x...
Forum: The Pipeline 10-30-2012, 02:37 PM
Replies: 103
Views: 135,455
Posted By aeonsim
I see they've got a booth at ASHG, hopefully some...

I see they've got a booth at ASHG, hopefully some of you who are attending will give them some stick about the commercial release of minion and the lack of released data!
Forum: Bioinformatics 08-30-2012, 10:29 PM
Replies: 7
Views: 8,055
Posted By aeonsim
Based on the SNP Validation work we've done the...

Based on the SNP Validation work we've done the QUAL score is pretty meaningless as a filter for Valid snps. We've had SNPs with a QUAL of 17 turn out to be real while SNPs with a QUAL of 60000 fail....
Forum: Bioinformatics 08-01-2012, 01:34 AM
Replies: 24
Views: 3,794
Posted By aeonsim
Also might be worth checking with your sequence...

Also might be worth checking with your sequence provider to make sure they sent you the right dataset.
Forum: Bioinformatics 06-28-2012, 04:59 AM
Replies: 6
Views: 1,708
Posted By aeonsim
Real time genomics (rtg) commercial great for...

Real time genomics (rtg) commercial great for trios
Freebayes
Samtools

Are other good tools.
Forum: Bioinformatics 06-09-2012, 07:16 PM
Replies: 42
Views: 10,570
Posted By aeonsim
It is commercial though there was at least until...

It is commercial though there was at least until recently, a free version with a few limitations on it. Can't find the link on there website any more though so your'd have to contact them to find out...
Forum: Bioinformatics 06-09-2012, 04:56 PM
Replies: 42
Views: 10,570
Posted By aeonsim
We have done a fair bit of independent evaluation...

We have done a fair bit of independent evaluation using your wgsim app and other metrics. We noted similar results to what you posted for BWA and Novoalign with rtg being similar to BWA overall but...
Forum: Bioinformatics 06-09-2012, 07:25 AM
Replies: 42
Views: 10,570
Posted By aeonsim
Accuracy is important but there are times and...

Accuracy is important but there are times and places where performance is more important. Otherwise everyone would probably be using Novoalign based on the various ROCs I've seen. While unfortunately...
Forum: Bioinformatics 06-07-2012, 03:45 AM
Replies: 42
Views: 10,570
Posted By aeonsim
Possibly interesting but like the others until...

Possibly interesting but like the others until one can see ROCs comparing it to the other aligners to see where the trade offs are it's just another aligner. Percentage of Reads aligned is a pretty...
Forum: Bioinformatics 06-07-2012, 03:30 AM
Replies: 3
Views: 1,172
Posted By aeonsim
One way not using the database is to download a...

One way not using the database is to download a dbsnp VCF file and then use bedtools to do a intersect with a bed or GTF file of human exomes.
Showing results 1 to 25 of 45

 


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