[julihepple]

Hello there Next genners

Hi there,

I am from South Africa (Cape Town) and we have just acquired some shiny new Next Gen machines. I work at the Central Analytical facility-DNA sequencing unit at Stellenbosch University and will be the lab tech for the next gen platforms. We have done quite a few runs on the PGM and are very happy with the results!!! Now to start tackling the SOLiD...

Hope to be reading some very insightful and helpful posts on this site!

Happy sequencing.

Juli

[pmcqt]

Hi folks,

My name is Philippe, i'm from france and i work as a reserach engineer at IGBMC (Strasbourg), i'm involved in all omics project in the lab. I'm dealing with microarrays an RNASeq studies at the moment.

[Chirag]

Making sense of Cuffdiff on bio replicates of RNA (treated under various conditions)

Hi all,

I have a single end 76 bp RNA from RNASeq, where RNA was treated with various drugs and have biological 5 replicates of each.

Scenario:
RNA Type-1 (No treatment) 5 replicates of each
RNA Type-2 (Treatment-1) 5 replicates of each
RNA Type-3 (Treatment-2) 5 replicates of each

I used tophat (to map to the genome) and cufflink (to construct the transcript), and recovered most annotated gene-models and identifies some new ones. I am interested in finding up and down regulated genes.

Then i use Cuffmerge to combine these transcripts from all 15 samples.

To get up/down-regulated genes, i used Cuffdiff. I got a lot of transcript, which cuffdiff reports as up/down regulated.


Normally, i would like to have a geneA (from control), which is significantly up/down regulated in treatment 1 and treatment2, and similar pattern in all other replicates . However, what i get is slightly different.

I rather find this gene-A (from control) is up/down regulated with treatment-1 and treatment-2 (which is good), but this enrichment is present in only some of the replicate sample, but not in all replicates.

Sometimes, this gene-A is significantly up/down regulated within control or within treatment. This makes the scenario even more complex. So, now, this gene-A can be significantly up/down regulated in within control (in few replicates) and also be significantly up/down regulated with treatment I and treatment II (but only in some replicates).

How to make better sense out of this ?

Thank you for your help in advance !!

regards
Chirag

[Chirag]

Hello !

Hi Guys !
I am Chirag, currently doing my PhD at UiB, Norway.
I am currently working on ncRNA and trying to figure out their roles during vertebrate embryogenesis.

[nirwalniraj]

Hello_small RNA sequencing

Hello to all,
I am new user of illumina genome analyzer platform. i am making library for small RNA by using v 1.5 illumina small RNA kit. The expected band on the agilent bioanalyzer is 92 and 100 bp but i am getting either nearly 100 or 106-08 bp bands in different samples. If any body have any idea about such observation. Please let me know whether I should go for the sequencing with these samples or not. I run the native 6% DNA PAGE gel for band seperation and i got only single band in gel near 100 bp and not two aas expected. It is of C. elegans sample.

[laibaofeng]

hi,all

I come from China.As a newer of NGS field,i almost know nothing about it! So i hope that i can obtain much more knowledge here .
Now i am working on Illumina platform, developing genome wide SNP markers of wheat.So i am looking forward to know any informations about this!
Thanks all!!!

[mjb_2902]

Hi there!

I'm new to this forum. My interests are in amplicon 454 pyrosequencing of 16S rDna. I have some experience running samples on the Titanium.

[sommeh]

Hallo all,

I am a molecular geneticist from Nairobi Kenya. Currently I am using ngs tools to understand the genetics underlying host pathogen interactions.The data includes genome sequences from 454, RNA-Seq from SOLiD and SNP data from SNP illumina arrays. This forum will be great to seek exchange and support.

Best regards,

[5tgb]

Hello!
I recently joined the Sales team of a service provider. Prior to this I was a researcher in molecular biology.
This is a great forum, lots of resources to keep up-to-date with the latest technologies. Thank you1

[pcturner57]

Greetings

Hi SEQanswers community,
I'm Pete Turner, and have been working with 454 and next-gen Illumina data for about 2 years. I've put together 2 complete bacterial genomes (E. coli) and they are soon to be published. Bridging all the gaps from insertion sequences was a major challenge, and was greatly helped by using optical restriction maps.
Newer work has focused on another 8 genomes. The plan is to identify mutations and tie in the results with RNA expression data from microarrays.
I'm hoping to assist others with sequence assembly as a consultant, for a reasonable hourly fee.
Cheers,
Pete

[vpa]

Greetings,
I'm a Research Associate at University o Guelph, ON Canada sequencing plasmids using 454 GS Junior. Seqanswers is great place to look for answers and I am excited to be in this forum.
Cheers,
vpa

[Vilhelm84]

Howdy

I am currently looking into influence of wobble positions on splicing and splicing fidelity. Doing my first deepseq analysis. Site looks great so far. Hope to help and be help as time goes on!

[Tobias Kockmann]

Hello

Hello SEQanswers community,

justed joined and wanted to say HELLO to everyone! Today I got 200 million reads from a multiplexed RNA-seq run on the HiSeq 2000 - but all the barcodes are NNNNNN A great reason to join, don't you think!?

Greetings,
Tobi

[Joyce Faler]

Analyzing transcriptome from 454 using Newbler

Hi, brand new to unix, Newbler & 454 generated data. I will be downloading pertinent software to a Mac G5 running OS X this week to get started. I expect to spend a lot of time surfing this community to get my feet wet & my project off the ground!
Cheers,
-Joyce

[velezbermudez]

Hello everyone!....my name is Isabel, I am doing a PhD in Molecular Genetics in Barcelona, Spain. I am working with maize actually in ChIP-Seq of a TF and I am glad to be in this community