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Search: Posts Made By: Jean
Forum: Bioinformatics 03-10-2014, 10:33 AM
Replies: 2
Views: 1,485
Posted By Jean
It's mainly visual, but JalView should give you a...

It's mainly visual, but JalView should give you a conservation score for a position over a MSAS
Forum: Sample Prep / Library Generation 03-07-2014, 08:13 AM
Replies: 9
Views: 4,102
Posted By Jean
We've used the Epicentre ScriptSeq2 kit for 50ng...

We've used the Epicentre ScriptSeq2 kit for 50ng of mRNA with good results
Forum: Bioinformatics 07-05-2013, 05:29 AM
Replies: 5
Views: 2,344
Posted By Jean
Hi. We have an RNAseq tool we are working on...

Hi.
We have an RNAseq tool we are working on called ALDEx (ANOVA-like Differential Expression) which will infer expression and variance per group. If you'd like to give it a try it is available as...
Forum: Bioinformatics 07-05-2013, 05:24 AM
Replies: 5
Views: 2,344
Posted By Jean
Hi. We have an RNAseq tool we are working on...

Hi.
We have an RNAseq tool we are working on called ALDEx (ANOVA-like Differential Expression) which will infer variance per sample and per group. If you'd like to give it a try it is available as...
Forum: Bioinformatics 04-18-2013, 07:07 AM
Replies: 1
Views: 1,262
Posted By Jean
Well, poly-A enrichment for bacterial RNA will...

Well, poly-A enrichment for bacterial RNA will not work because the RNA molecules are not typically poly-adenylated unless for degradation. You will have to do some kind of mRNA enrichment/rRNA...
Forum: Site Feedback/Suggestions 04-01-2013, 07:39 AM
Replies: 1
Views: 6,159
Posted By Jean
Site is super laggy?

For the past week the seqanswers site has been like molasses for me. Takes minutes to load a single page. Is anyone else having lag issues or is this something on my end?
Forum: RNA Sequencing 01-28-2013, 06:14 AM
Replies: 2
Views: 2,128
Posted By Jean
What kind of samples are these (origin,...

What kind of samples are these (origin, collection)? Could it be bacterial RNA? Esp. 16s/23s seq that would be highly repeated.
Forum: Illumina/Solexa 12-18-2012, 08:58 AM
Replies: 23
Views: 9,378
Posted By Jean
How much PhiX spike-in?

How much PhiX spike-in?
Forum: Bioinformatics 12-04-2012, 08:33 AM
Replies: 7
Views: 6,592
Posted By Jean
FastQC works well

FastQC works well
Forum: Metagenomics 11-22-2012, 12:08 PM
Replies: 15
Views: 10,777
Posted By Jean
Hi Nick. I've read your blog post from Aug 2012...

Hi Nick.
I've read your blog post from Aug 2012 and I'm just wondering about what your current strategies are for amplicon sequencing on the MiSeq? Have you found a better approach?
Forum: Sample Prep / Library Generation 11-14-2012, 06:37 AM
Replies: 0
Views: 1,344
Posted By Jean
Size-selection with ScriptSeq v2 RNAseq Library?

We want to use the ScriptSeq v2 RNA-seq Library prep kit (Epicentre) to make libraries for some rRNA-depleted bacterial RNA. Looking through the protocol I don't see any option for a size-selection....
Forum: Illumina/Solexa 09-04-2012, 07:31 AM
Replies: 2
Views: 1,893
Posted By Jean
So you are only mapping to the "3 draft genomes"...

So you are only mapping to the "3 draft genomes" you got from the assembly and ignoring the rest? How much of your genomic data is represented in these drafts? If you map back the metagenomic reads...
Forum: Illumina/Solexa 07-25-2012, 06:33 AM
Replies: 4
Views: 2,055
Posted By Jean
Illumina error is LOWER than 454 as far as I...

Illumina error is LOWER than 454 as far as I remember. The problem is the PCR error that you will see pop up more in Illumina typically only because you are sequencing much deeper than 454.

I also...
Forum: SOLiD 07-18-2012, 08:13 AM
Replies: 5
Views: 2,587
Posted By Jean
You can not convert colorspace to basespace...

You can not convert colorspace to basespace directly. See here why:
http://seqanswers.com/forums/showpost.php?p=59156&postcount=4
Forum: Illumina/Solexa 07-11-2012, 10:10 AM
Replies: 2
Views: 1,230
Posted By Jean
Looks like a custom R plot. You'd have to learn...

Looks like a custom R plot. You'd have to learn to use R:
http://www.r-project.org/

Very powerful and worth learning for graphics and statistics.
Forum: Bioinformatics 07-10-2012, 06:22 AM
Replies: 11
Views: 3,709
Posted By Jean
Couldn't this be plotted in R with the mapping...

Couldn't this be plotted in R with the mapping and transcriptome information?
Forum: Bioinformatics 07-10-2012, 05:59 AM
Replies: 5
Views: 3,801
Posted By Jean
You probably don't want to compare e-values....

You probably don't want to compare e-values. Since the e-value depends on the size of the database you can't directly compare between different datasets.
Forum: Bioinformatics 06-27-2012, 06:47 AM
Replies: 15
Views: 5,301
Posted By Jean
Hi Simon, I totally agree with your points and...

Hi Simon,
I totally agree with your points and replicates are absolutely necessary to make any conclusions. Just an addendum though - adding more samples (replicates or not) DOES increase the...
Forum: Bioinformatics 05-28-2012, 09:03 AM
Replies: 22
Views: 4,773
Posted By Jean
Hi Simon, Sorry to hijack this but I can't find...

Hi Simon,
Sorry to hijack this but I can't find the posts referring to this. How do you recommend dealing with equally multiply-mapped reads? Count only unique maps and discard the others?
Forum: General 05-25-2012, 09:00 AM
Replies: 2
Views: 2,728
Posted By Jean
This may not be relevant since the topic is old,...

This may not be relevant since the topic is old, but the cufflinks model is not useful for bacterial RNAseq analysis because of it's isoform-based assumptions. You would want to use something along...
Forum: Metagenomics 05-10-2012, 10:25 AM
Replies: 3
Views: 3,317
Posted By Jean
It depends on what the population is (how diverse...

It depends on what the population is (how diverse for example), and how "deep" you want to sequence (do you care about rare bugs?)
Forum: General 04-18-2012, 03:07 PM
Replies: 11
Views: 5,141
Posted By Jean
Blog/Wiki format is good for me. You can copy...

Blog/Wiki format is good for me. You can copy code snippets, link files, upload images, and make notes.
Forum: RNA Sequencing 03-07-2012, 11:42 AM
Replies: 10
Views: 2,641
Posted By Jean
By hiccups I meant statistical hiccups. When the...

By hiccups I meant statistical hiccups. When the variation in your replicates is very high, you will violate some of the assumptions for the differential expression test. Whatever method/analysis you...
Forum: RNA Sequencing 03-06-2012, 10:46 AM
Replies: 10
Views: 2,641
Posted By Jean
Just to get it started I can try to answer some...

Just to get it started I can try to answer some of your points:



If your questions is "what genes are uniquely/differentially expressed in tissue B" then I'd say yes this is valid. However,...
Forum: Ion Torrent 03-06-2012, 10:28 AM
Replies: 5
Views: 5,506
Posted By Jean
I believe the OP is attempting a...

I believe the OP is attempting a meta-transcriptomic experiment (mRNAseq), not a 16S profiling.
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