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Search: Posts Made By: MattB
Forum: Bioinformatics 05-05-2015, 05:37 AM
Replies: 2
Views: 977
Posted By MattB
Thanks! That is correct, we are using...

Thanks!

That is correct, we are using TopHat2.

I have also been debating what 'uniquely' means, I guess it comes down to where you set a threshold ;)
Forum: Bioinformatics 05-05-2015, 04:23 AM
Replies: 2
Views: 977
Posted By MattB
Filter unique hits in Bowtie2 for stranded RNA-seq

Hi all,

We have PE stranded RNA-seq data, and we want to filter the alignment files for uniquely mapping reads (ie. no multi-hit reads).

We have done this before for 'unstranded' data based on...
Forum: Sample Prep / Library Generation 03-04-2013, 11:00 PM
Replies: 0
Views: 1,681
Posted By MattB
Multiplexing on Fluidigm Access Array

Hi all,

Just wondering if anyone has pushed the Fluidigm Access Array beyond a level of a 10 amplicon multiplex (the 'official' upper limit)?

Matt
Forum: Sample Prep / Library Generation 02-25-2013, 04:39 AM
Replies: 13
Views: 2,757
Posted By MattB
Thanks, wondering how far we could push a PCR...

Thanks, wondering how far we could push a PCR multiplex if we tried to include hundreds of amplicons...
Forum: Sample Prep / Library Generation 02-24-2013, 10:47 PM
Replies: 13
Views: 2,757
Posted By MattB
Caprice, I am talking about SNPs. We could of...

Caprice, I am talking about SNPs. We could of course 'genotype' with Affymetrix/Illumina/Sequenom/Fluidigm etc., or do GBS/RAD/ddRAD sequencing as a random sampling of SNPs, but I am particularly...
Forum: Sample Prep / Library Generation 02-21-2013, 11:13 PM
Replies: 13
Views: 2,757
Posted By MattB
Thanks Vinz, so the mutliplexing/barcoding isn't...

Thanks Vinz, so the mutliplexing/barcoding isn't an issue, just the super-high PCR multiplexing challenge remains (if we want 1000+ amplicons). However, with a high-fidelity enzyme like the NEB Q5 or...
Forum: Sample Prep / Library Generation 02-21-2013, 10:43 PM
Replies: 13
Views: 2,757
Posted By MattB
Still chewing over various options...in principle...

Still chewing over various options...in principle it should be possible with 'Ampliseq' or Fluidigm Access Array too (documented 10 amplicon multiplex x 48 so 480 potential amplicons per chip)....
Forum: Sample Prep / Library Generation 02-13-2013, 12:16 AM
Replies: 13
Views: 2,757
Posted By MattB
1500 amplicons in salmon

Hi all,

Basically my goal is to 'genotype' 1500 loci in salmon through sequencing. Had initially though of RAD/GBS/ddRAD/etc, however then I realised that one can in theory just do targeted...
Forum: Bioinformatics 05-31-2012, 02:02 AM
Replies: 77
Views: 25,016
Posted By MattB
Thanks, I had actually planned to use the Galaxy...

Thanks, I had actually planned to use the Galaxy option but our local installation is undergoing some maintenance at the moment hence I was after a simple script alternative.

The Perl script that...
Forum: Bioinformatics 05-30-2012, 11:46 PM
Replies: 77
Views: 25,016
Posted By MattB
Ah, that looks promising, will give it a go....

Ah, that looks promising, will give it a go. Don't know why my google search didn't hit upon that one! ;)

Thanks!
Forum: Bioinformatics 05-30-2012, 11:21 PM
Replies: 77
Views: 25,016
Posted By MattB
Thanks for quick reply. Actually, I'm looking for...

Thanks for quick reply. Actually, I'm looking for something even simpler, where I just have one interleaved fastq file that I want to split into separate forward and reverse. Probably should have...
Forum: Bioinformatics 05-30-2012, 10:21 PM
Replies: 77
Views: 25,016
Posted By MattB
Just wondering if anyone has a script to do the...

Just wondering if anyone has a script to do the opposite to the scripts in this thread, ie. split an already interleaved forward and reverse file into separate forward and reverse files (for Casava...
Forum: De novo discovery 03-30-2010, 07:33 AM
Replies: 38
Views: 15,015
Posted By MattB
There is a setting in SOAPdenovo that I thought...

There is a setting in SOAPdenovo that I thought had some influence on this, used when you run 'SOAPdenovo contig' separately.

-M mergeLevel(default 1,min 0, max 3): the strength of merging...
Forum: De novo discovery 03-30-2010, 07:14 AM
Replies: 38
Views: 15,015
Posted By MattB
I think overall the de novo assemblers handle...

I think overall the de novo assemblers handle SNPs quite OK (at least from my experience with CLC; Abyss and SOAPdenovo). I think SOAPdenovo chooses one of the SNP alleles at random for the contig...
Forum: De novo discovery 03-26-2010, 03:47 AM
Replies: 38
Views: 15,015
Posted By MattB
Well, you'll definitely pick up polymorphic SNPs...

Well, you'll definitely pick up polymorphic SNPs in the 16 animal family...and I'd suspect they'll probably be polymorphic in other individuals/populations unless there are dramatic genetic...
Forum: De novo discovery 03-25-2010, 05:28 AM
Replies: 38
Views: 15,015
Posted By MattB
Good points there. In our case, we were not too...

Good points there. In our case, we were not too concerned about rare alleles, in fact we planned to avoid those SNPs!

I don't think I've really mentioned it above, but in our case the goal was to...
Forum: De novo discovery 03-25-2010, 05:15 AM
Replies: 38
Views: 15,015
Posted By MattB
yep, agree with lletourn that the optimal...

yep, agree with lletourn that the optimal strategy very much depends on what type of SNPs you want to find and what you want to do with them afterwards ;)
Forum: De novo discovery 03-25-2010, 05:06 AM
Replies: 38
Views: 15,015
Posted By MattB
We will be using paired-end 75bp Illumina reads...

We will be using paired-end 75bp Illumina reads for our next project, since we believe the higher sequence output will outweigh the longer read lengths of 454. Ultimately, if you are just trying to...
Forum: De novo discovery 03-02-2010, 10:44 PM
Replies: 38
Views: 15,015
Posted By MattB
We just joined the contigs in the order they were...

We just joined the contigs in the order they were output by the denovo assember, so essentially at random. Since I posted that however, I have been using the CLC NGS Cell software to perform de novo...
Forum: Bioinformatics 01-18-2010, 06:29 AM
Replies: 10
Views: 2,231
Posted By MattB
Wei, have a look at Galaxy...

Wei, have a look at Galaxy (http://main.g2.bx.psu.edu/)

It has a very user friendly interface for the Fastx tools..
Forum: Bioinformatics 01-18-2010, 05:53 AM
Replies: 10
Views: 2,231
Posted By MattB
Looks like strob just beat me to it ;)

Looks like strob just beat me to it ;)
Forum: Bioinformatics 01-18-2010, 05:52 AM
Replies: 10
Views: 2,231
Posted By MattB
Hi Wei, Have a look at the 'FASTX...

Hi Wei,

Have a look at the 'FASTX Statistics' and 'FASTQ Quality Chart' programs that are part of the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). They provide a nice way to...
Forum: Illumina/Solexa 01-03-2010, 11:22 PM
Replies: 1
Views: 3,378
Posted By MattB
Hi Wei, Try the Fastx toolkit ...

Hi Wei,

Try the Fastx toolkit

http://hannonlab.cshl.edu/fastx_toolkit/

Matt
Forum: De novo discovery 11-18-2009, 10:18 PM
Replies: 38
Views: 15,015
Posted By MattB
Boonie, it depends on the type of genotyping...

Boonie, it depends on the type of genotyping assay (ie. number of SNPs) that are interested in. For the Illumina Infinium iSelect assay, Illumina specify minimum 50bp on EITHER side of the SNP for...
Forum: De novo discovery 11-16-2009, 04:52 AM
Replies: 38
Views: 15,015
Posted By MattB
I'd be suspicious about SNPs only found on the...

I'd be suspicious about SNPs only found on the last one or two bases of your reads (I posted a separate thread on this), as they could well be remnants of adaptor sequence (adaptor trimming won't...
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