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Forum: Sample Prep / Library Generation 11-17-2014, 11:11 PM
Replies: 5
Views: 1,244
Posted By Jeremy
Transcriptome sequencing for differential...

Transcriptome sequencing for differential expression is basically high throughput qPCR. You can't get qPCR published without biological replicates, if you tried to published qPCR with a single pool...
Forum: Bioinformatics 09-15-2014, 02:54 AM
Replies: 1
Views: 1,574
Posted By Jeremy
Your problem is probably from this line ...

Your problem is probably from this line

geneList <- factor(as.integer(geneNames %in% myInterestingGenes))

geneNames %in% myInterestingGenes will return a vector of TRUE / FALSE of length...
Forum: RNA Sequencing 08-28-2014, 08:53 PM
Replies: 15
Views: 20,884
Posted By Jeremy
For differential expression analysis, I wouldn't....

For differential expression analysis, I wouldn't. That design would have a lot of trouble getting published. For almost the same price you can sequence biological replicates that have been...
Forum: RNA Sequencing 08-28-2014, 08:28 PM
Replies: 15
Views: 20,884
Posted By Jeremy
Based on my quote marks I think I was asking the...

Based on my quote marks I think I was asking the OP what they meant and then pointing out (via rhetorical question) that you can't get within group variance using a pooled approach. But it was so...
Forum: Bioinformatics 08-05-2014, 08:26 PM
Replies: 34
Views: 12,445
Posted By Jeremy
A more functional alternative to cygwin would be...

A more functional alternative to cygwin would be bio-linux (ubuntu with many programs such as samtools pre installed) in a virtual box.
Forum: Bioinformatics 07-31-2014, 06:29 PM
Replies: 2
Views: 1,892
Posted By Jeremy
Bowtie(1) needs a Bowtie(1) library, it can't use...

Bowtie(1) needs a Bowtie(1) library, it can't use a Bowtie2 library. Assuming you already have Bowtie installed then make the library using the 'bowtie-build' command. You should upgrade to bowtie2...
Forum: Bioinformatics 07-24-2014, 02:04 AM
Replies: 3
Views: 1,210
Posted By Jeremy
Check out the program SNPeff...

Check out the program SNPeff (http://snpeff.sourceforge.net/).
Forum: Bioinformatics 07-23-2014, 02:49 AM
Replies: 2
Views: 2,031
Posted By Jeremy
Because the result is the data after it has been...

Because the result is the data after it has been corrected for library size. E.g. if one sample had 20M reads and the other had 16M reads then they can't be compared directly. DESeq corrects for this...
Forum: Bioinformatics 07-18-2014, 02:19 AM
Replies: 24
Views: 12,373
Posted By Jeremy
The topic of this thread was plant mitochondrial...

The topic of this thread was plant mitochondrial genome assembly. In any case, have you subsetted your data to get only the mitochondrial sequence? Based on the number of reads you are talking about...
Forum: Bioinformatics 07-18-2014, 01:28 AM
Replies: 24
Views: 12,373
Posted By Jeremy
If you are talking about a mammalian...

If you are talking about a mammalian mitochondrial genome maybe. Plant mitochondrial genomes are very very different.
Forum: Bioinformatics 07-18-2014, 12:38 AM
Replies: 24
Views: 12,373
Posted By Jeremy
How can you reconstruct the genome using...

How can you reconstruct the genome using transcriptome data?
Forum: Bioinformatics 07-17-2014, 07:56 PM
Replies: 24
Views: 12,373
Posted By Jeremy
You need to use a transcriptome assembler...

You need to use a transcriptome assembler (SOAPdenovo-Trans, Trinity, Trans-abyss etc.), of course a genome assembler will fail with RNA-seq data, almost all of the assumptions regarding the data are...
Forum: Bioinformatics 07-15-2014, 07:38 PM
Replies: 43
Views: 24,337
Posted By Jeremy
Those are two different tests, but you are...

Those are two different tests, but you are overwriting the first reslt object (res) with the second.

res <- nbinomTest( cds, "A-mock", "A-infect", )
res <- nbinomTest( cds, "B-mock", "B-infect",...
Forum: The Pipeline 07-14-2014, 08:51 PM
Replies: 51
Views: 169,846
Posted By Jeremy
Nothing is ever the sole factor of consideration....

Nothing is ever the sole factor of consideration. And in my experience, money is ALWAYS a limiting factor, as usual it is a trade off. Pac Bio and hopefully Oxford Nanopore have a huge advantage in...
Forum: Bioinformatics 07-01-2014, 01:23 AM
Replies: 1
Views: 1,008
Posted By Jeremy
Blast2GO is pretty good for that, I don't think...

Blast2GO is pretty good for that, I don't think it will identify fusion transcripts though.
Forum: Bioinformatics 05-27-2014, 09:11 PM
Replies: 2
Views: 801
Posted By Jeremy
call that string MyString NewString <-...

call that string MyString
NewString <- paste("mygenes_", MyString, sep="")

If that is a column of a data frame called DF
DF$MyString <- paste("mygenes_", DF$MyString, sep="")
Forum: Bioinformatics 05-21-2014, 02:41 AM
Replies: 4
Views: 2,345
Posted By Jeremy
I think R needs to be compiled with tcl/tk...

I think R needs to be compiled with tcl/tk already installed. Some packages need the dev version of tcl/tk and won't work with the normal version.

What does R say when you give it:...
Forum: Illumina/Solexa 05-15-2014, 10:59 PM
Replies: 8
Views: 6,123
Posted By Jeremy
The TruSeq DNA PCR-Free kit claims to have...

The TruSeq DNA PCR-Free kit claims to have "Superior genomic coverage with radically reduced library bias and gaps" compared to the original TruSeq DNA kits. I have been recommended to do multiple...
Forum: Bioinformatics 05-08-2014, 02:14 AM
Replies: 2
Views: 1,050
Posted By Jeremy
It might be more effective to exclude...

It might be more effective to exclude mitochondrial sequence after the assembly, the mitochondria and chloroplast tend to form separate contigs anyway. Unless your plant species is Arabidopsis, only...
Forum: Bioinformatics 05-08-2014, 01:55 AM
Replies: 24
Views: 12,373
Posted By Jeremy
With plant mitochondria you aren't necessarily...

With plant mitochondria you aren't necessarily expecting a single cyclic strand of DNA (for example:...
Forum: Ion Torrent 04-17-2014, 12:33 AM
Replies: 2
Views: 2,085
Posted By Jeremy
bamtools convert can convert bam to fastq

bamtools convert can convert bam to fastq
Forum: Bioinformatics 04-02-2014, 08:40 PM
Replies: 6
Views: 1,516
Posted By Jeremy
You want to plot 3.2 billion data points? That is...

You want to plot 3.2 billion data points? That is going to be a problem. You should look into some other way of representing that data.

If you do want to plot with R then I reccomend the ggbio...
Forum: Bioinformatics 04-02-2014, 08:31 PM
Replies: 6
Views: 1,098
Posted By Jeremy
lets assume that table with the annotation is...

lets assume that table with the annotation is called "annot" and it has the comumn with the An01g00010 entries also called "ID" the you want:
New <- merge(res.combined,annot,by="ID",all.x=T,sort=F)...
Forum: RNA Sequencing 03-28-2014, 12:27 AM
Replies: 6
Views: 3,218
Posted By Jeremy
The object res has the results for all of the...

The object res has the results for all of the genes and their FDR adjusted p-values. I always just merge res with the corrected count data and then write it all out to a tab delimited table then you...
Forum: RNA Sequencing 03-26-2014, 08:38 PM
Replies: 6
Views: 3,218
Posted By Jeremy
at which step?

at which step?
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