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Forum: RNA Sequencing 08-04-2015, 07:14 AM
Replies: 1
Views: 1,004
Posted By warrenemmett
Using PolyA+ to identify/quantify lncRNAs?

Hi,

In some recent publications I have seen people quantifying lncRNA using polyA+ data (this is from primary data generated for the study). As far as I'm aware there are lncRNA that have polyA...
Forum: Bioinformatics 09-30-2013, 09:43 AM
Replies: 0
Views: 1,326
Posted By warrenemmett
Average coverage for miRNAseq analysis for mouse/human ?

Hi there,

I recently got asked to take a look at some miRNA data from mouse, 6 samples with 1 million reads each off a Miseq.

I am mostly interested in quantification and presence of known...
Forum: Bioinformatics 04-11-2013, 05:53 AM
Replies: 0
Views: 1,365
Posted By warrenemmett
Cuffcompare codes and use in novel non-coding gene discovery

Hi,

I'm looking into lincRNA discovery and working through some cuffcompare output for a number of samples.

I am curious whether people use these in discovery pipelines as hard filters ? I...
Forum: Bioinformatics 04-03-2013, 09:07 AM
Replies: 16
Views: 5,839
Posted By warrenemmett
Hi there, Thanks for the reply. Yes I saw...

Hi there,

Thanks for the reply. Yes I saw their paper and came to the same conclusion. The nail in the coffin is that they do not include any of their scripts which essentially means redoing most...
Forum: Bioinformatics 04-03-2013, 05:57 AM
Replies: 16
Views: 5,839
Posted By warrenemmett
CircRNA discovery tools

Hi,

Circular RNA has become a hot topic recently, I know there are several papers but none that I've found that include the software pipeline they used.

If anyone is willing to provide a tool...
Forum: Bioinformatics 10-18-2011, 12:31 PM
Replies: 0
Views: 2,760
Posted By warrenemmett
dbSNP updates and the effect on variant annotation results

Hi there,

I have had several queries from users checking my snp annotations (i use both ANNOVAR and SNPeff) and tell me that a large percentage of their candidate SNPs that are called as unknown...
Forum: Bioinformatics 10-12-2011, 02:08 AM
Replies: 2
Views: 2,552
Posted By warrenemmett
Hi, Sorry I was looking at the genome build...

Hi,

Sorry I was looking at the genome build in UCSC rather than the annotation. From ENSEMBL it looks like cow is the only one with variation information so I guess that is the better choice.
Forum: Bioinformatics 10-11-2011, 02:48 AM
Replies: 2
Views: 2,552
Posted By warrenemmett
Best annotated mamalian genome, excluding human/mouse/rat

Hi there,

We are currently doing some research on what species to use for a polymorphism sequencing project on mammal bone. We are ideally looking at non-human to avoid contamination and need...
Forum: Bioinformatics 09-28-2010, 07:56 AM
Replies: 16
Views: 6,331
Posted By warrenemmett
Would you mind elaborating on this? I cannot see...

Would you mind elaborating on this? I cannot see the difference between having novoalign running a first-pass fast alignment to map the majority of reads (if mapped incorrectly here wouldnt the reads...
Forum: Bioinformatics 09-27-2010, 04:07 AM
Replies: 16
Views: 6,331
Posted By warrenemmett
Specifically concerning RNA-seq analysis. The new...

Specifically concerning RNA-seq analysis. The new tools to align spliced reads (such as MapSplice) are show to be more sensitive than Tophat (mentioned earlier) and I was wondering if in this case...
Forum: Bioinformatics 09-27-2010, 01:00 AM
Replies: 3
Views: 2,347
Posted By warrenemmett
Thank you for the response! I have heard of...

Thank you for the response!

I have heard of Novoalign and its reputation but I was hoping that there was a newer, open source algorithm available to replace MAQ, mostly because I want to use it...
Forum: Bioinformatics 09-26-2010, 07:08 AM
Replies: 3
Views: 2,347
Posted By warrenemmett
MAQ and quality scores during alignment

Hi,

I have seen some recent papers using MAQ and assume it is because it includes quality information?

Do you know of any better open source software that does this? I initially thought that...
Forum: General 09-01-2010, 05:35 AM
Replies: 0
Views: 2,347
Posted By warrenemmett
Quality scores and sequence alignment

Hi,

I recently had a discussion with someone about the use of quality scores in alignment (specifically related to SNP discovery). As far as I remember there was some debate but at the time most...
Forum: Bioinformatics 10-11-2009, 11:42 PM
Replies: 6
Views: 3,752
Posted By warrenemmett
tophat, not producing rpkm values with -G option

Hi there,

I'm running a medaka 75bp paired end dataset through tophat. I am currently using the ensembl genome and the ensembl genome annotation. However I get the following output when I run it....
Forum: Bioinformatics 09-18-2009, 07:11 AM
Replies: 13
Views: 15,960
Posted By warrenemmett
Although there are definitely many more reads...

Although there are definitely many more reads mapped for single-end, when I look at the rpkm values the paired end data, produces values 100-300 higher (just browsed through the top few...
Forum: Bioinformatics 09-16-2009, 03:45 AM
Replies: 13
Views: 15,960
Posted By warrenemmett
Thanks for the reply! I had the same suspicion...

Thanks for the reply! I had the same suspicion and after more searching have found the bug :)

Thanks again for the help!
Forum: Bioinformatics 09-15-2009, 07:01 AM
Replies: 13
Views: 15,960
Posted By warrenemmett
Can paired-end mapping produce more reads than single-end ?

Hi,

I am currently mapping 75bp paired end data to a cDNa library. I have heard that there is a chance there are chimeras in a large portion of the reads and as such have had to change to single...
Forum: Bioinformatics 08-17-2009, 05:47 AM
Replies: 0
Views: 2,260
Posted By warrenemmett
Converting genbank accession to UCSC

Hi there,

I am having some difficulty finding where I can convert genbank accessions to UCSC accessions (both on a small and a large scale). Please let me know if you know of simple ways to do...
Forum: RNA Sequencing 06-15-2009, 12:46 AM
Replies: 2
Views: 6,553
Posted By warrenemmett
Hi there, How I did it, although there is...

Hi there,

How I did it, although there is definitely a better way. I downloaded the UCSC knowngene table for human in BED format and converted it to GFF2 (through GALAXY). I then converted that to...
Forum: RNA Sequencing 04-14-2009, 11:10 PM
Replies: 10
Views: 20,220
Posted By warrenemmett
Hi Ali, Thanks for the response. I have...

Hi Ali,

Thanks for the response. I have checked out TopHat which also looks like quite an interesting package. I was wondering as well about using something like 454 with ERANGE since the read...
Forum: RNA Sequencing 04-09-2009, 07:13 AM
Replies: 10
Views: 20,220
Posted By warrenemmett
At the moment I'm just checking out whats...

At the moment I'm just checking out whats available so I'd be interested in any packages that process RNA data. I'm looking for a package that attributes reads to a gene then calculates statistics...
Forum: Introductions 04-09-2009, 01:03 AM
Replies: 1
Views: 1,625
Posted By warrenemmett
hello

Hi there,

I'm currently working in a biotech company in Italy and my interest and work revolves around next-gen sequencing so I regularly visit this forum to check what the people with more...
Forum: RNA Sequencing 04-09-2009, 12:11 AM
Replies: 10
Views: 20,220
Posted By warrenemmett
ERANGE and other packages for RNAseq analysis

Hi everyone,

I am currently exploring the ERANGE package and was wondering whether there are other available packages like this to identify new regions and calculate statistics based on read...
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