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Forum: RNA Sequencing 09-18-2013, 09:56 AM
Replies: 0
Views: 1,215
Posted By Eric Fournier
Question rDNA and RNA-Seq

Hello,

I am currently analyzing sequencing data of total RNA from mouse samples. As can be expected in total RNA, I have quite a bit of ribosomal sequences. However, when aligning to my genome...
Forum: RNA Sequencing 05-14-2013, 06:35 AM
Replies: 4
Views: 6,912
Posted By Eric Fournier
Hello Dan, we ran our samples on five...

Hello Dan,

we ran our samples on five different lanes. Each lane used 6 of 8 possible multiplex tags from the Encore multiplex kit (which uses 4nt tags). This actually caused a small problem,...
Forum: RNA Sequencing 05-10-2013, 06:30 AM
Replies: 4
Views: 6,912
Posted By Eric Fournier
Thank you very much! The article was a very nice...

Thank you very much! The article was a very nice read.
Forum: RNA Sequencing 05-08-2013, 12:33 PM
Replies: 4
Views: 6,912
Posted By Eric Fournier
Normalizing with ERCC spike-in

Hello everyone,

I have RNA-seq libraries prepared from 10 different stages of embryonic development (3 replicates per stage), with each library constructed using the same number of embryos. The...
Forum: RNA Sequencing 01-23-2013, 10:30 AM
Replies: 9
Views: 5,812
Posted By Eric Fournier
I've finally managed to get reasonable results...

I've finally managed to get reasonable results using Tophat2 by quality trimming my reads. Even though the low-quality read ends were accurate enough for BLAT/BLAST to align them properly, they...
Forum: RNA Sequencing 01-18-2013, 05:20 AM
Replies: 9
Views: 5,812
Posted By Eric Fournier
Alright, I'll try those. I've tried using...

Alright, I'll try those.

I've tried using STAR, but unfortunately I don't have enough RAM to run it, even in sparse mode. I've started looking into using Amazon Web Services or getting some time...
Forum: RNA Sequencing 01-17-2013, 12:54 PM
Replies: 9
Views: 5,812
Posted By Eric Fournier
I've moved on from using Trimmomatic to cutadapt,...

I've moved on from using Trimmomatic to cutadapt, and I've been able to clean up my sequences pretty well. However, I'm running into a new snag: I just can't seem to reliably align spliced reads.
...
Forum: RNA Sequencing 01-14-2013, 11:37 AM
Replies: 9
Views: 5,812
Posted By Eric Fournier
Trouble with Trimmomatic

I've now spent quite a fair amount of time trying to clean up my sequences with Trimmomatic, but I've been unable to find a set of parameters that gets rid of most of the Illumina adapter sequences....
Forum: RNA Sequencing 01-10-2013, 11:19 AM
Replies: 9
Views: 5,812
Posted By Eric Fournier
Suggested aligner for local alignment of RNA-seq data

Greetings,

I'm trying to analyze the results of Illumina RNA sequencing (~5x150M 100bp PE reads). One problem that we are facing is that for a very large number of our reads, only the first ~50bp...
Forum: Bioinformatics 01-17-2012, 06:09 AM
Replies: 2
Views: 1,978
Posted By Eric Fournier
To anyone coming across this thread because they...

To anyone coming across this thread because they can't figure out how to set Scripture's -windows flag (Which is listed as optional in the documentation, but seems mandatory when running...
Forum: Bioinformatics 01-17-2012, 06:08 AM
Replies: 17
Views: 5,897
Posted By Eric Fournier
To anyone coming across this thread because they...

To anyone coming across this thread because they can't figure out how to set Scripture's -windows flag (Which is listed as optional in the documentation, but seems mandatory when running...
Forum: Bioinformatics 07-27-2011, 08:04 AM
Replies: 7
Views: 3,617
Posted By Eric Fournier
What you want to do is not what assemblers are...

What you want to do is not what assemblers are meant to do, so it's not surprising that none of them behave as you expect them to. Assemblers are meant to assemble genomes/transcriptomes out of...
Forum: Bioinformatics 07-26-2011, 07:49 AM
Replies: 7
Views: 3,617
Posted By Eric Fournier
Your question does not make sense. If you...

Your question does not make sense.

If you want to know where your primers would fit on your sequences, then you need to BLAT/BLAST/Some-Alignment-Tool them. This is not an assembly problem, and...
Forum: Bioinformatics 07-26-2011, 05:30 AM
Replies: 7
Views: 3,617
Posted By Eric Fournier
You could use a program like SEQClean to remove...

You could use a program like SEQClean to remove the primers from your sequences. This should increase the quality of your assembly.
Forum: Bioinformatics 07-21-2011, 05:08 AM
Replies: 2
Views: 1,639
Posted By Eric Fournier
For anyone who would stumble on this post and...

For anyone who would stumble on this post and wonder what the solution is:

sff_extract is a python script. It needs to be run with the python interpreter.
Forum: Bioinformatics 07-21-2011, 05:04 AM
Replies: 12
Views: 9,008
Posted By Eric Fournier
Do you have the genome of a closely related...

Do you have the genome of a closely related organism that you could use as a backbone? If so, search for "backbone" in the MIRA3 reference.
Forum: Bioinformatics 07-18-2011, 04:54 AM
Replies: 11
Views: 2,965
Posted By Eric Fournier
Read the error message attentively. "chrom names...

Read the error message attentively. "chrom names are case sensitive" should give you a hint. You changed your chromosome names from "chr6" to "6". In the UCSC genome browser, chromosome names take...
Forum: Bioinformatics 07-18-2011, 04:18 AM
Replies: 11
Views: 2,965
Posted By Eric Fournier
The error essage plainly states that your start...

The error essage plainly states that your start coordinate is larger than your end coordinates. Reverse them.

In the UCSC genome browser, coordinates are always specified in increasing order,...
Forum: General 07-05-2011, 07:49 AM
Replies: 0
Views: 1,347
Posted By Eric Fournier
Mapping vs De Novo & Masking or not

Greetings,

for the past year, I've been involved in a project aiming to study the effects that Artificial Reproduction Techniques (ART) have on bovine embryos. Amongst the many experiments that...
Forum: Bioinformatics 07-05-2011, 05:23 AM
Replies: 2
Views: 11,152
Posted By Eric Fournier
The transcriptome consists of all that is...

The transcriptome consists of all that is transcribed, ie all RNA species including mRNA, miRNA, tRNA, lncRNA, etc. It is usually studied through samples of RNA. You can get the basic idea by reading...
Forum: General 07-05-2011, 05:02 AM
Replies: 6
Views: 2,947
Posted By Eric Fournier
A bias toward UTRs might arise from the protocol...

A bias toward UTRs might arise from the protocol used to prepare your samples. For example, if you amplified your material using oligo-dT primers, you'll have a bias toward the 3'UTRs.
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