SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: smice
Forum: Epigenetics 06-02-2016, 02:31 AM
Replies: 9
Views: 3,539
Posted By smice
Thank you for the answers!

Thank you for the answers!
Forum: Epigenetics 05-28-2016, 11:05 AM
Replies: 9
Views: 3,539
Posted By smice
Thanks for the reply! And which kit would this...

Thanks for the reply! And which kit would this be? Have you tried it in practice? Do you know maybe how do they achieve this?

Nevertheless we still need someone to sequence it, so if anyone has...
Forum: Epigenetics 05-26-2016, 03:51 AM
Replies: 9
Views: 3,539
Posted By smice
Experienced sequencing providers for RRBS-seq?

Hi,

can someone recommend me a reliable sequencing provider for RRBS-sequencing? Our current provider struggles with this kind of application, they have problems finding the right amount of PhiX,...
Forum: Epigenetics 10-24-2011, 05:20 AM
Replies: 0
Views: 2,400
Posted By smice
Using MACS for histone marks with GLOBAL lambda

Hello everyone!

We are trying to use MACS for detecting enriched regions in a histone modification ChIPSeq experiment. I know that MACS is rather designed for transcription factors and sharp...
Forum: Bioinformatics 09-21-2011, 06:43 AM
Replies: 24
Views: 11,215
Posted By smice
Hello, I am no longer working for the company...

Hello, I am no longer working for the company developing the GenoViewer (Astrid Research Inc.), so I cannot speak in their name. When I left there was a clear intention to finish it (as you see, it...
Forum: Bioinformatics 09-21-2011, 12:02 AM
Replies: 5
Views: 3,206
Posted By smice
I did it all again, now with the debian package...

I did it all again, now with the debian package installation, just to be sure of the process, and I'd like to correct myself: apparently the key is to run the patch twice! Whether before or after...
Forum: Bioinformatics 09-20-2011, 06:23 AM
Replies: 5
Views: 3,206
Posted By smice
Yeah! It works! My problems finally got solved. ...

Yeah! It works! My problems finally got solved.
I highly recommend this patch for every MACS user.

However, I have a remark. The blog site says:



It suggests that you should patch before...
Forum: Bioinformatics 09-19-2011, 07:45 AM
Replies: 5
Views: 3,206
Posted By smice
I have encountered just the same problem. I have...

I have encountered just the same problem. I have a bunch of ELAND export files to run (s_#_export.txt), and MACS worked on some, but for others, it crashed with the error message described above....
Forum: Bioinformatics 11-17-2010, 03:49 AM
Replies: 26
Views: 14,466
Posted By smice
You mean, how ChIPSeq worked for the CNV data?...

You mean, how ChIPSeq worked for the CNV data? No, we haven't done any analyses, currently we are in the experiment designing phase, wondering whether we should develop a CNV detecting tool ourselves...
Forum: Bioinformatics 11-15-2010, 04:09 AM
Replies: 26
Views: 14,466
Posted By smice
Software tools for detecting Copy Number Variations (CNV)

Hello,

I'm currently interested in CNV (Copy Number Variation, but I'm sure you're familiar :)) detection, and I wonder

1. what software tools exist for this application? I've seen one package...
Forum: Bioinformatics 09-20-2010, 03:28 AM
Replies: 24
Views: 11,215
Posted By smice
That is because you can select different contigs...

That is because you can select different contigs from the fasta file and different contigs from the BAM file. The upper ones change the reference, the lower ones, below the separating line, change...
Forum: Bioinformatics 09-19-2010, 11:32 PM
Replies: 24
Views: 11,215
Posted By smice
What kind of assembly software do you use? I...

What kind of assembly software do you use? I assume its output can be converted to SAM/BAM. The file format itself of the SAM/BAM does allow the use of 454 reads, so technically it is undoubtedly...
Forum: Bioinformatics 09-19-2010, 11:10 PM
Replies: 24
Views: 11,215
Posted By smice
Yes, of course. The viewer is designed to...

Yes, of course. The viewer is designed to visualize assembly data stored in SAM/BAM files, no matter where the data came from, what kind of sequencing technology you used. Although note that the...
Forum: Bioinformatics 09-17-2010, 06:12 AM
Replies: 24
Views: 11,215
Posted By smice
We have just uploaded a newer version to the...

We have just uploaded a newer version to the GenoViewer site (http://www.GenoViewer.com). Please check it out, it contains various fixes and the annotation management is also redesigned (the change...
Forum: Bioinformatics 09-01-2010, 06:24 AM
Replies: 24
Views: 11,215
Posted By smice
lh3, that's a great comprehensive review, would...

lh3, that's a great comprehensive review, would you update it and include GenoViewer?

Well, "actual size" button has been renamed, you were right. It wouldn't be so useful assembly viewer if it...
Forum: Bioinformatics 08-26-2010, 06:58 AM
Replies: 24
Views: 11,215
Posted By smice
Dear maubp! Thank you for your remarks. Note...

Dear maubp!

Thank you for your remarks. Note that the software is a beta version and is still under development, some features are not working seamlessly and many features will be added in the...
Forum: Bioinformatics 08-25-2010, 02:46 AM
Replies: 24
Views: 11,215
Posted By smice
Exclamation GenoViewer: a new next generation sequencing viewer/browser is available now!

GenoViewer, the latest software developed by Astrid Research, Inc., is now available.

By developing GenoViewer, our aim was to develop a user-friendly viewer for NGS assembly data visualization,...
Forum: De novo discovery 07-08-2010, 01:30 AM
Replies: 8
Views: 8,699
Posted By smice
Hello, I am working for a Hungarian...

Hello,
I am working for a Hungarian bioinformatics company, and one of our main profiles is NGS data analysis, so I have some experience related to this topic. :) We are also putting together a...
Forum: General 06-25-2009, 01:21 AM
Replies: 26
Views: 7,599
Posted By smice
Thank you for your answer and the advices! ...

Thank you for your answer and the advices!

By the way, I know the question is vague, but the analysis of the bioinformatics market is not MY question. I would be most happy if I could focus on a...
Forum: General 06-19-2009, 01:22 AM
Replies: 26
Views: 7,599
Posted By smice
market research

Hello everyone!

I need some help. I have to introduce the growing market of bioinformatics (and ng sequencing data analysis, specifically) in a few pages, but I cannot really find any useful...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 09:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO