Another Newbie.. Anyone to advise.?

teutara · 03-05-2011, 01:50 PM

Dear All,

I am MS student from Turkey, interested in sequence assembly. I was told to design primers out of some sff files, and got almost no help about it(in person).
Thanks to google, i found mira-cap3 and ran it and got some contigs, then designed some primers out of them. My advisor quite like the output and the job i have done for now, and told me if i am interested in this topic, this could be my thesis.

While doing that job (for experts like you, it is trivial of course) i did read some manuals of existing assembly programs.

I am wondering what are the basic steps of this area, what kind of instructions to follow, etc..?
There are so many questions and most of them should be answered by my own effort of course, but where to dig to find the treasure?

I am trying to read articles about the topic i am asking, but there are so many gaps. One tells about north, another from south.
There might be some cookbooks, some recipes that can be followed i think.
There might tons of request like this one, but i thought i should give a try..

Any help will be greatly appreciated.
Thank you in advance,

Best,
Visam

flxlex · 03-06-2011, 11:15 PM

Moving to a more appropriate forum...

teutara · 03-07-2011, 12:23 AM

thanks flxflex,
have more hope to get answer on this, which i guess be helpful to some other people else of me..

Best,
Visam

rwenang · 03-07-2011, 12:44 AM

try "bioinformatics for dummies". it might help.

Jose Blanca · 03-16-2011, 01:12 AM

We do a little workshop for our students, the materials could be of some use to you.

http://bioinf.comav.upv.es/courses/sequence_analysis/

Regards.

shandley · 03-16-2011, 07:35 AM

Hi Visam,

This is a common problem. More and more biologists are beginning to gather vast amounts of sequencing data and looking for the best tools and techniques to mine this information. There are lots of on-line resources. You have already found one of the best resources in the SeqAnswers site.

Similar to Jose, we also offer a Workshop on genomic techniques. It was held for the first time this past January in the Czech Republic and covered a variety of topics (sequencing technologies, quality control, assembly, mapping, RNA-seq, metagenomics ...). We plan on holding a very similar Workshop in the same location next year. If this is of interest you can find more information here:

http://www.molecularevolution.org/

Good luck!

SAH

teutara · 03-16-2011, 12:04 PM

@ rwenang

thank you for your recommendation, in fact i read (not in detail) some bioinformatics books, trying to catch that topic, but unfortunately the ones i read were not so helpful.

@Jose Blanca

thank you for your interest, i did see your website earlier.
i guess it would not be inappropriate if ask a question,
i used one of your tools while assembling, the job i have done will take a part in a publication. Since i have to mention sff_extract, how should i cite it?

@shandley

thank you for your post. i gave a quick look at your website, do you share some documentary work, like some outlines of the main topics?
i discussed with my boss and he is encouraging me to attend some workshops, since i missed yours, can you recommend anything else? hope it is an ethical question?

Best,
Visam

shandley · 03-16-2011, 12:14 PM

Hi Visam,

Everything we have is on the web-site. Most of it is tailored for specific lessons. For more general tutorials, learning activities you will also want to make sure to check out each individual software's web-page. There are some great authors in this community that spend many thankless hours developing documentation to their individual software packages.

We are hosting Workshops in Comparative Genomics and in Molecular Evolution this coming Summer in Fort Collins, CO, USA. More information is here:

http://www.molecularevolution.org/node/316

Fort Collins might be a stretch for you. If you can wait, we are planning on hosting a similar Workshop that we did last January in the same location (Cesky Krumlov in the Southern Bohemia region of the Czech Republic). Cesky Krumlov is about 3 hours from Prague or Vienna, so getting in and out is not a big problem. We will have details about this Workshop on the web-site in the coming months. I will also post a general announcement about the Workshop on this web-site. You can always contact me directly with any questions.

This web-site is a good resource for other Workshop and Course offerings. You can check the specific forums on this subject "Events / Conferences". Let me know if you have any other questions.

SAH

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03-05-2011, 01:50 PM	#1
teutara Junior Member Location: turkey, izmir Join Date: Jan 2011 Posts: 4	Another Newbie.. Anyone to advise.? Dear All, I am MS student from Turkey, interested in sequence assembly. I was told to design primers out of some sff files, and got almost no help about it(in person). Thanks to google, i found mira-cap3 and ran it and got some contigs, then designed some primers out of them. My advisor quite like the output and the job i have done for now, and told me if i am interested in this topic, this could be my thesis. While doing that job (for experts like you, it is trivial of course) i did read some manuals of existing assembly programs. I am wondering what are the basic steps of this area, what kind of instructions to follow, etc..? There are so many questions and most of them should be answered by my own effort of course, but where to dig to find the treasure? I am trying to read articles about the topic i am asking, but there are so many gaps. One tells about north, another from south. There might be some cookbooks, some recipes that can be followed i think. There might tons of request like this one, but i thought i should give a try.. Any help will be greatly appreciated. Thank you in advance, Best, Visam Last edited by teutara; 03-05-2011 at 01:59 PM.

03-06-2011, 11:15 PM	#2
flxlex Moderator Location: Oslo, Norway Join Date: Nov 2008 Posts: 415	Moving to a more appropriate forum...

03-07-2011, 12:23 AM	#3
teutara Junior Member Location: turkey, izmir Join Date: Jan 2011 Posts: 4	thanks flxflex, have more hope to get answer on this, which i guess be helpful to some other people else of me.. Best, Visam

03-07-2011, 12:44 AM	#4
rwenang Member Location: Singapore Join Date: Jan 2009 Posts: 31	try "bioinformatics for dummies". it might help.

03-16-2011, 01:12 AM	#5
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	We do a little workshop for our students, the materials could be of some use to you. http://bioinf.comav.upv.es/courses/sequence_analysis/ Regards.

03-16-2011, 07:35 AM	#6
shandley Member Location: Saint Louis, MO Join Date: Sep 2010 Posts: 58	Hi Visam, This is a common problem. More and more biologists are beginning to gather vast amounts of sequencing data and looking for the best tools and techniques to mine this information. There are lots of on-line resources. You have already found one of the best resources in the SeqAnswers site. Similar to Jose, we also offer a Workshop on genomic techniques. It was held for the first time this past January in the Czech Republic and covered a variety of topics (sequencing technologies, quality control, assembly, mapping, RNA-seq, metagenomics ...). We plan on holding a very similar Workshop in the same location next year. If this is of interest you can find more information here: http://www.molecularevolution.org/ Good luck! SAH

03-16-2011, 12:04 PM	#7
teutara Junior Member Location: turkey, izmir Join Date: Jan 2011 Posts: 4	@ rwenang thank you for your recommendation, in fact i read (not in detail) some bioinformatics books, trying to catch that topic, but unfortunately the ones i read were not so helpful. @Jose Blanca thank you for your interest, i did see your website earlier. i guess it would not be inappropriate if ask a question, i used one of your tools while assembling, the job i have done will take a part in a publication. Since i have to mention sff_extract, how should i cite it? @shandley thank you for your post. i gave a quick look at your website, do you share some documentary work, like some outlines of the main topics? i discussed with my boss and he is encouraging me to attend some workshops, since i missed yours, can you recommend anything else? hope it is an ethical question? Best, Visam

03-16-2011, 12:14 PM	#8
shandley Member Location: Saint Louis, MO Join Date: Sep 2010 Posts: 58	Hi Visam, Everything we have is on the web-site. Most of it is tailored for specific lessons. For more general tutorials, learning activities you will also want to make sure to check out each individual software's web-page. There are some great authors in this community that spend many thankless hours developing documentation to their individual software packages. We are hosting Workshops in Comparative Genomics and in Molecular Evolution this coming Summer in Fort Collins, CO, USA. More information is here: http://www.molecularevolution.org/node/316 Fort Collins might be a stretch for you. If you can wait, we are planning on hosting a similar Workshop that we did last January in the same location (Cesky Krumlov in the Southern Bohemia region of the Czech Republic). Cesky Krumlov is about 3 hours from Prague or Vienna, so getting in and out is not a big problem. We will have details about this Workshop on the web-site in the coming months. I will also post a general announcement about the Workshop on this web-site. You can always contact me directly with any questions. This web-site is a good resource for other Workshop and Course offerings. You can check the specific forums on this subject "Events / Conferences". Let me know if you have any other questions. SAH