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Forum: RNA Sequencing 10-03-2012, 01:00 PM
Replies: 6
Views: 2,401
Posted By clostridium40
I have spoken to several people that have done...

I have spoken to several people that have done DSN normalization for their RNA-seq experiments, and they have all confirmed that the high expressing genes stay that way. So apparently you should...
Forum: RNA Sequencing 09-10-2012, 04:00 PM
Replies: 6
Views: 2,401
Posted By clostridium40
DSN Normalization vs Ribo-Zero

We are looking to do some RNA-seq projects using Illumina for bacterial gene expression, and we are trying to decide between ribo-depleting with RiboZero and using Epicentre's ScriptSeq kits. Or my...
Forum: Bioinformatics 10-21-2011, 11:36 AM
Replies: 0
Views: 1,200
Posted By clostridium40
Repetitive Element Resolution Software

I was wondering if anyone has worked with a couple of the software programs developed by JGI/LANL to automatically resolve repetitive elements in genomes, such as "Polisher" or "dubFinisher"...
Forum: Bioinformatics 10-19-2011, 01:52 PM
Replies: 2
Views: 2,880
Posted By clostridium40
I have done a couple of bacterial genomes (~5.5...

I have done a couple of bacterial genomes (~5.5 Mb) as hybrid de novo assemblies using Newbler 2.6, I started with 112k paired end + 307k single end 454 reads at that resulted in 344 contigs with an...
Forum: Illumina/Solexa 09-23-2011, 12:33 PM
Replies: 20
Views: 16,182
Posted By clostridium40
Phillip This is great information, very...

Phillip

This is great information, very helpful for planning out your RNA-seq experiments (which I'm learning is critical). I was wondering if you have observed a number of indexes (bar codes)...
Forum: Pacific Biosciences 09-21-2011, 12:24 PM
Replies: 10
Views: 6,307
Posted By clostridium40
What is your overall impression of PacBio RS?...

What is your overall impression of PacBio RS? What are the pros and cons you have seen? If you can, how would you compare it to other technologies?
Forum: 454 Pyrosequencing 09-13-2011, 09:17 AM
Replies: 9
Views: 4,332
Posted By clostridium40
Thanks for the recommendation, I will definitely...

Thanks for the recommendation, I will definitely try SSPACE and see if we can close some of the gaps in the genome.
Forum: RNA Sequencing 09-09-2011, 04:10 PM
Replies: 2
Views: 2,969
Posted By clostridium40
Direct sequencing of mRNA for RNA-seq

I was told today by our collaborators that they have found that directly sequencing the mRNA gives them better results then converting to cDNA when they do RNA-seq. Has anyone else found this to be...
Forum: Bioinformatics 09-08-2011, 02:38 PM
Replies: 0
Views: 2,078
Posted By clostridium40
IMAGE: Iteratively Mapping and Assembly for Gap Elimination software

I was just wondering if anyone has worked with the IMAGE software, and if so what were their experiences with it. I've had a little trouble getting it to work properly, and was just wondering if...
Forum: Bioinformatics 09-02-2011, 02:23 PM
Replies: 0
Views: 1,277
Posted By clostridium40
Determining Repeat Sequences

So, I'm working with a several bacterial genomes, and I'm learning bioinformatics as I work, so forgive me if this is a dumb question. My genomes have a lot of repeat sequences (for a prokaryotic...
Forum: RNA Sequencing 07-29-2011, 09:20 AM
Replies: 4
Views: 4,805
Posted By clostridium40
Phillip, Thanks for the valuable...

Phillip,

Thanks for the valuable information. I have one other question, the Illumina kit does ribo-depletion based on poly-A tails on the mRNA right? So, I'm working with prokaryotic mRNA, so do...
Forum: RNA Sequencing 07-28-2011, 06:15 PM
Replies: 4
Views: 4,805
Posted By clostridium40
Illumina RNA-Seq Preparations

I'm just getting into RNA-Seq, and had a question about the library preparations for Illumina HiSeq. I know that Illumina sells a kit that will take the isolated mRNA samples and convert them to...
Forum: 454 Pyrosequencing 07-26-2011, 11:11 AM
Replies: 8
Views: 3,185
Posted By clostridium40
kmcarr - you are a life saver, I can't thank you...

kmcarr - you are a life saver, I can't thank you enough for all your help. Thank you, very very much appreciated.
Forum: 454 Pyrosequencing 07-26-2011, 10:43 AM
Replies: 8
Views: 3,185
Posted By clostridium40
I ran the command, and you're correct that it was...

I ran the command, and you're correct that it was not installed properly for my system and that is the problem, I got:

/usr/local/genome/bin/sfffile: ELF 64-bit LSB executable, x86-64, version 1...
Forum: 454 Pyrosequencing 07-26-2011, 09:13 AM
Replies: 8
Views: 3,185
Posted By clostridium40
kmcarr, I'm running Ubuntu 11.04 32-bit OS,...

kmcarr,

I'm running Ubuntu 11.04 32-bit OS, the files were given to me on a jump drive and I copied them and moved the executable file into my $PATH variable. I used the command sfffile, however...
Forum: 454 Pyrosequencing 07-25-2011, 05:23 PM
Replies: 8
Views: 3,185
Posted By clostridium40
sff file problems

I'm trying to separate and trim the MIDs off my reads from my .sff files using the sfffile that is provided by Roche. However, every time that I attempt to execute the program it gives me the...
Forum: Bioinformatics 07-20-2011, 01:57 PM
Replies: 2
Views: 1,859
Posted By clostridium40
Ignore this post, another newbie who had hit a...

Ignore this post, another newbie who had hit a wall, but I figured out the answer.
Forum: Bioinformatics 07-19-2011, 02:05 PM
Replies: 2
Views: 1,859
Posted By clostridium40
sff_extract problems

You will have to forgive me but I know very little about Linux and python, I have installed MIRA in order to assemble 454 reads and Illumina reads from a couple of bacterial genomes. However, before...
Forum: 454 Pyrosequencing 07-14-2011, 12:47 PM
Replies: 9
Views: 4,332
Posted By clostridium40
Improving 454 assembly with Illumina

I working on de novo sequencing of 6 bacterial strains that have a genome size ~5.5 Mb each. I have had them sequenced using 454, but only had about ~15x coverage, which left a lot of contigs. I...
Forum: 454 Pyrosequencing 06-22-2011, 03:30 PM
Replies: 7
Views: 3,853
Posted By clostridium40
Thanks sklages, I really appreciate the...

Thanks sklages,

I really appreciate the advise. I will get the SFF Tools and will look into the MIRA3 assembler. Thanks again
Forum: Introductions 06-22-2011, 10:33 AM
Replies: 0
Views: 946
Posted By clostridium40
Hello

Just wanted to say "Hello" to everyone, and glad to see this wonderful site up and running as I will probably have many questions in the near future. I'm a post doctorate researcher, and have some...
Forum: 454 Pyrosequencing 06-22-2011, 09:35 AM
Replies: 7
Views: 3,853
Posted By clostridium40
454 Sequencing Assembly/MIDs

I'm fairly new to 454 sequencing and genome assembly, and I currently have six bacterial genomes that were sequenced whole shotgun sequencing and pair-end sequenced. They were done together with the...
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