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Forum: Ion Torrent 10-10-2015, 06:55 AM
Replies: 28
Views: 56,437
Posted By avilella
Any news on the price per gigabase on each of...

Any news on the price per gigabase on each of these? 520, 530 and 540 runs?
Forum: Epigenetics 09-09-2015, 09:54 AM
Replies: 4
Views: 3,438
Posted By avilella
As an additional note to the previous answer, the...

As an additional note to the previous answer, the duplicate rate will increase the deeper you sequence a given sample.

The curve of total reads and total distinct reads will depend on the...
Forum: Illumina/Solexa 10-17-2014, 05:09 AM
Replies: 73
Views: 350,252
Posted By avilella
1) They can form two clusters next to each other....

1) They can form two clusters next to each other. The BaseCalling algorithms in the machine will determine if they are clonal or not based on the signal coming from each cycle and consider them as...
Forum: Bioinformatics 01-06-2013, 02:14 AM
Replies: 3
Views: 852
Posted By avilella
It's a column-based format separated by tabs. For...

It's a column-based format separated by tabs. For visualization purposes, if you want to pipe the tab-separated columns into something that looks pretty on the screen, in Linux you can use 'column...
Forum: Site Feedback/Suggestions 08-09-2011, 05:06 AM
Replies: 1
Views: 3,281
Posted By avilella
Mentioning seqanswers in paper acknowledgements

Just found this paper on Nature Genetics that mentions seqanswers in the acknowledgements:

... and SeqAnswers online forum (see URLs) for advice on genome assembly and visualization.

Cool!
Forum: Sample Prep / Library Generation 07-20-2011, 02:31 AM
Replies: 0
Views: 1,805
Posted By avilella
maximum size sonicated DNA?

What is the maximum DNA size people can reliably obtain when sonicating genomic DNA? I've seen papers that claim they can sonicate to 2-5Kb and then do protein-DNA pulldown on those 2-5 Kb DNA...
Forum: SOLiD 07-15-2011, 03:58 AM
Replies: 1
Views: 1,834
Posted By avilella
Has anyone had access to ABI 5500xl System with 0.75 μm nanobeads?

This has supposedly been available since June or July. Has anyone had access to ABI 5500xl System with 0.75 μm nanobeads?
...
Forum: Site Feedback/Suggestions 06-17-2011, 12:27 AM
Replies: 0
Views: 3,265
Posted By avilella
Synergy between seqanswers.com and biostar.stackexchange.com?

Hi,

I am an avid user of both seqanswers.com and biostar.stackexchange.com and I would like to suggest that both sites benefit from the content it's being created in both sites. There are many...
Forum: Illumina/Solexa 05-06-2011, 12:55 AM
Replies: 73
Views: 350,252
Posted By avilella
spreadsheet with updated specs

Hi all,

Illumina has officially announced the updated specs for their Hiseq2000 and Hiseq1000 machines, with throughput up to 600GB. I've updated a google spreadsheet I keep with all the specs for...
Forum: General 04-27-2011, 06:33 AM
Replies: 37
Views: 17,470
Posted By avilella
454 plans to launch a new sequencing chemistry...

454 plans to launch a new sequencing chemistry for the GS FLX that will reach read lengths to 750 bases and beyond. Supposedly by the end of June...
Forum: Illumina/Solexa 01-28-2011, 02:22 AM
Replies: 74
Views: 45,397
Posted By avilella
Has anyone done the math on the price per base...

Has anyone done the math on the price per base one would get with a 2x150bp run on the MiSeq and the HiSeq, taking into account library prep costs?

People working medium-sized genomes (10-100 MBp)...
Forum: RNA Sequencing 10-28-2010, 12:19 AM
Replies: 2
Views: 2,064
Posted By avilella
I asked this question to the EBI SRA people, and...

I asked this question to the EBI SRA people, and I was told that both NCBI and EBI SRA apply a series of QC procedures before they store the sequences. If you see any noise in the data, like...
Forum: SOLiD 09-08-2010, 10:55 AM
Replies: 40
Views: 8,683
Posted By avilella
Solid 4HQ?

Does anybody know if the solid 4hq is anywhere close to being released or if anybody has any idea of the day-to-day throughput of the machine?
Forum: Bioinformatics 09-05-2010, 08:26 AM
Replies: 13
Views: 14,589
Posted By avilella
There are two utilities that I am missing in...

There are two utilities that I am missing in current methods: I am using cdbfasta/cdbyank to index fastq files, but I would like to be able to compress the fastq file so that it takes up less space,...
Forum: Bioinformatics 07-30-2010, 02:15 AM
Replies: 12
Views: 4,602
Posted By avilella
I think one of the challenges in transcriptome...

I think one of the challenges in transcriptome assembly is to correctly reconstruct paralogous genes so that one doesn't end up creating chimeric transcripts. This is specially troublesome for...
Forum: The Pipeline 07-20-2010, 04:51 AM
Replies: 9
Views: 6,887
Posted By avilella
More PacBio specs

These come straight from the source, Dr. Steven T. Lott gave a talk at the Wellcome Trust Genome Campus (2010-Jul-20).

They have 80K "wells" (not sure the term is right) in each cell, and cells...
Forum: Bioinformatics 05-10-2010, 01:19 AM
Replies: 7
Views: 3,908
Posted By avilella
Hi ssing, I've recently been working on a...

Hi ssing,

I've recently been working on a method to cluster transcriptome reads and reconstruct cDNA models for species that don't have a reference genome, using existing gene family information...
Forum: General 04-06-2010, 12:30 AM
Replies: 21
Views: 6,527
Posted By avilella
I can be added as a HYPERLINK to the number, like...

I can be added as a HYPERLINK to the number, like this:

=HYPERLINK ( "http://www3.appliedbiosystems.com/cms/groups/global_marketing_group/documents/generaldocuments/cms_078637.pdf" ; 100)

Then...
Forum: General 04-05-2010, 02:16 AM
Replies: 35
Views: 11,786
Posted By avilella
I think the difference between the ~1500 reported...

I think the difference between the ~1500 reported by Illumina and the 540 (as of 20100405) in the HTS website comes mainly from people not being aware of the site, rather than from being reluctant to...
Forum: RNA Sequencing 03-20-2010, 03:46 AM
Replies: 0
Views: 1,778
Posted By avilella
Anyone with Solexa RNA-seq 150+bp for non-model sps with no close reference genome?

Hi,

I am working on a method to cluster and assemble RNA-seq data for species that don't have a close genome reference. For example, a species for which the closest available whole-genome assembly...
Forum: General 03-19-2010, 04:05 AM
Replies: 35
Views: 11,786
Posted By avilella
Maybe we then need a phone picture of the Serial...

Maybe we then need a phone picture of the Serial number as a proof :-)
Forum: General 03-19-2010, 03:59 AM
Replies: 35
Views: 11,786
Posted By avilella
Awesome initiative! As an incentive to...

Awesome initiative!

As an incentive to reports, a prize should be given to the person who reported the highest id at the end of each week (Friday 5pm CET). T-shirt? Chocolate bar?
Forum: Bioinformatics 03-18-2010, 02:01 AM
Replies: 0
Views: 1,660
Posted By avilella
distance measure to compare peak set profiles in chip-seq datasets

Hi,

Is there any tool that will tell me how different/similar two chip-seq peak sets are in two different parts of the genome?

E.g. if I have a ~10Kb region in the genome with a series of peaks...
Forum: Bioinformatics 03-18-2010, 01:59 AM
Replies: 32
Views: 32,509
Posted By avilella
comparing peak set profiles in chip-seq datasets

Hi,

Is there any tool that will tell me how different/similar two chip-seq peak sets are in two different parts of the genome?

E.g. if I have a ~10Kb region in the genome with a series of peaks...
Forum: General 03-09-2010, 01:22 AM
Replies: 5
Views: 2,816
Posted By avilella
After a bit of inquiring, I've added the price at...

After a bit of inquiring, I've added the price at 500k for both GAIIx and HiSeq2000 from Illumina. If anyone knows of a better estimate for it, feel free to update the spreadsheet:
...
Showing results 1 to 25 of 34

 


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