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Forum: Oxford Nanopore 12-15-2017, 08:12 AM
Replies: 4
Views: 2,012
Posted By vebaev
A Nanopore run - budget/cost?

As I'm not familiar with the whole protocol of a Nanopore run, can someone more experienced list the consumables/costs for a project concerning the run of unknown plant species genome DNA?

I'm...
Forum: Service Providers 12-08-2015, 03:39 AM
Replies: 1
Views: 2,397
Posted By vebaev
smallRNA-seq company in Europe

Can someone recommend me a reliable company with low price for small RNAs in Europe.
For now I did not found cheaper than 400 euro per sample (10M reads).
Forum: Bioinformatics 05-07-2013, 06:02 AM
Replies: 1
Views: 719
Posted By vebaev
Commercial software help?

Hi,
I have some limited budget that I have to spend for a software this month (~1000$) and I'm stuck to CLC Main WB or Geneious and both of them have cons: clc MWB does not do NGS but can use it for...
Forum: Bioinformatics 12-04-2012, 12:56 AM
Replies: 7
Views: 2,631
Posted By vebaev
In some cases people add am offset value so they...

In some cases people add am offset value so they can filter out the this noise from low counts, but if I have RPKM how and at which point I can add an offset value to each condition?
Forum: Bioinformatics 12-04-2012, 12:02 AM
Replies: 7
Views: 2,631
Posted By vebaev
Not to open a new topic, so I have similar...

Not to open a new topic, so I have similar issues, I just made my RPKM values for my 3 samples (no replicates), and I started comparing them ...making folds and log2

I have 2 question:
1. should...
Forum: Bioinformatics 11-16-2012, 05:23 AM
Replies: 2
Views: 1,285
Posted By vebaev
Thanks! I also noticed: Error:...

Thanks!

I also noticed:


Error: 2012-Nov-16 14:48:07: No such file or directory: /home/milev/CASAVA_v1.8.2/src/c++/lib/alignment/BclReader.cpp(86): Throw in function unsigned int...
Forum: Bioinformatics 11-16-2012, 02:02 AM
Replies: 2
Views: 1,285
Posted By vebaev
BCL converter error

Hi all,

I'm trying to get the fast file from our demo PhiX run and I have some error in the nohup.out after make -j command

here is the output - http://pastebin.com/x0VT9vEx

so I got empty...
Forum: Events / Conferences 08-15-2012, 01:21 AM
Replies: 11
Views: 4,576
Posted By vebaev
2 weeks till the abstract deadline, do not wait...

2 weeks till the abstract deadline, do not wait the last minute :D

We are placing 4 discounted tickets for early registrations via Paypal (if you are unable to make wire transfer) -...
Forum: Events / Conferences 08-13-2012, 02:55 AM
Replies: 11
Views: 4,576
Posted By vebaev
Please note: Registration fee includes hotel...

Please note: Registration fee includes hotel accommodation (4-star all-inclusive) :D

Sunny Day Black sea Resort

http://web.uni-plovdiv.bg/vebaev/venue.png
Forum: Events / Conferences 08-09-2012, 02:21 AM
Replies: 11
Views: 4,576
Posted By vebaev
WE ARE EXTENDING THE ABSTRACT DEADLINE AND EARLY...

WE ARE EXTENDING THE ABSTRACT DEADLINE AND EARLY REGISTRATION FEE DUE TO PEOPLE REQUEST!

DEADLINE NOW: 29 AUGUST!

Enjoy! :)

PS
@Gillmaner , thanks for the post :)
Forum: Events / Conferences 08-04-2012, 09:59 AM
Replies: 11
Views: 4,576
Posted By vebaev
Save ~15% from the early registration fee till 20...

Save ~15% from the early registration fee till 20 August with your abstract to BIOCOMP BG 2012!

http://biocomp.bio.uni-plovdiv.bg/

Limited time offer ~15% OFF

Early Standard Academic fee -...
Forum: Events / Conferences 07-18-2012, 01:11 PM
Replies: 11
Views: 4,576
Posted By vebaev
See who will give a talk at BIOCOMP BG 2012...

See who will give a talk at BIOCOMP BG 2012 conference! Do not forget to submit your abstract until 20 August at:
http://biocomp.bio.uni-plovdiv.bg/
...
Forum: Introductions 06-28-2012, 09:29 AM
Replies: 2
Views: 748
Posted By vebaev
of course this forum is for discussion, there we...

of course this forum is for discussion, there we can have fun along our coffee together :)
Forum: Introductions 06-28-2012, 08:09 AM
Replies: 2
Views: 748
Posted By vebaev
A Facebook NGS place :)

Hi guys :)

just a sec ago I made a FB page for NGS (since I dodnt found existing one) where we can join, everybody is welcome :D

http://www.facebook.com/NextGenerationSequencing
Forum: Bioinformatics 06-28-2012, 01:11 AM
Replies: 15
Views: 8,497
Posted By vebaev
I do not remember for copy number but from our...

I do not remember for copy number but from our plant samples from more than 80 000 assembled contigs we identified not more than 20 miR precursors which is quite bad maybe they are not so stable...
Forum: Bioinformatics 06-27-2012, 06:37 AM
Replies: 15
Views: 8,497
Posted By vebaev
In RNA-seq you cannot find miRNAs, you can...

In RNA-seq you cannot find miRNAs, you can capture precursors of miRNAs with quite low abundance comparing to protein-coding transcripts.
Forum: RNA Sequencing 06-26-2012, 12:35 PM
Replies: 36
Views: 23,135
Posted By vebaev
yes one of the plants is tomato but other samples...

yes one of the plants is tomato but other samples we have plants with no ref genome/annotation
Forum: RNA Sequencing 06-26-2012, 12:26 PM
Replies: 36
Views: 23,135
Posted By vebaev
no, each 2 are different plant, 1 control and 1...

no, each 2 are different plant, 1 control and 1 treatment , no info of transcriptome size (probably only one of them will be sequenced with ref genome - tomato)
Forum: RNA Sequencing 06-26-2012, 12:16 PM
Replies: 36
Views: 23,135
Posted By vebaev
And if we came back on the topic :) what is the...

And if we came back on the topic :) what is the optimal number of millions reads for de novo RNA-seq without reference genome? as if we have 12 samples per 6 lanes = ~15M for sample is this OK for...
Forum: RNA Sequencing 06-26-2012, 09:38 AM
Replies: 36
Views: 23,135
Posted By vebaev
Thanks. The goal is to compare 2 samples of...

Thanks.
The goal is to compare 2 samples of RNA-seq of unsequenced plant, so we do not know the size of the transcriptome. What should be the optimal M reads for this de novo RNA-seq task?
I asked...
Forum: RNA Sequencing 06-26-2012, 08:51 AM
Replies: 36
Views: 23,135
Posted By vebaev
Not to open a new tread for my question: I...

Not to open a new tread for my question:

I was wondering what is the optimal number of samples per lane on GAIIx if we want to do an RNA-seq of unsequenced plant?
Forum: Events / Conferences 06-22-2012, 08:10 AM
Replies: 11
Views: 4,576
Posted By vebaev
NOTE! For a limited time 22 June-22 July you...

NOTE!
For a limited time 22 June-22 July you can register and save 10% off from the Standart Academic Fee (400 euro) which includes accommodation in 4-star All-inclusive Sunny Day Black Sea resort,...
Forum: Events / Conferences 06-21-2012, 02:20 AM
Replies: 11
Views: 4,576
Posted By vebaev
BAYER is sponsoring our conference! Do not forget...

BAYER is sponsoring our conference! Do not forget to register! :)
Forum: RNA Sequencing 06-19-2012, 10:05 AM
Replies: 1
Views: 946
Posted By vebaev
small RNA sample peak at 16nt?

Dear all,
besides some normal peaks of 21-22nt small/miR RNAs we had observed peaks at 16-17nt? did anybody have experience what can cause such effect?



Thanks
Forum: Illumina/Solexa 05-24-2012, 05:54 AM
Replies: 9
Views: 1,669
Posted By vebaev
Thanks @huguesparri and what about doing an...

Thanks @huguesparri and what about doing an RNA-seq for 6 conditions each on a separate lane? What you suggest SE PE lenght?
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