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Old 04-02-2012, 03:15 AM   #361
oliviajm
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Location: france

Join Date: Apr 2012
Posts: 13
Default Hi from France

Hello everybody,

I'm from Lille, North of France. I work on NGS since 1 month only, but I hope for a long time.

Thanks for this very useful forum.
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Old 04-02-2012, 03:35 AM   #362
rathankar
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Location: chennai, Bangalore

Join Date: Oct 2011
Posts: 10
Default

dear friends
I am new member for NGS analysis and have the following data. any help would be appreciated from the members or the administrator of the group
1. i am working on mus musculus and in building the indexes, bowtie takes a long time, more than 2 days for all the chromosomes. instead of building the indexes together, which takes a long time for buffering, can i build it one by one?. it takes hardly 25 mins for a single chromosome indexing and hence one can build the indexes for all the chromosomes within 500 mins or less than 10 hrs. pls reply

with regards
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Old 04-03-2012, 01:13 PM   #363
tusharbiot
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Location: India

Join Date: Feb 2012
Posts: 7
Default

Hi to all

I am a doctoral student, assembling partial fosmid libraries and organellar genome from the plant family Zingiberaceae.
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Old 04-04-2012, 10:44 PM   #364
Virology
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Location: PRC

Join Date: Apr 2012
Posts: 1
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Hi everybody
I am a virology graduate student, preparing to do a whole genome sequence project using 454.
Good luck!
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Old 04-06-2012, 09:07 AM   #365
wesserg
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Location: University of Warsaw - Poland/ GHSU - USA, Augusta GA

Join Date: Feb 2012
Posts: 4
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Hi everyone!

Mathematics and statistics. Recently (2009) switched to applications in biology and genetics. What a mess we got here!

University of Warsaw (Poland), Georgia Health Sciences University (USA), Florida State University (USA).
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Old 04-06-2012, 11:39 PM   #366
AllanLindh
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Location: Santa Cruz, CA, USA, Earth

Join Date: Apr 2012
Posts: 5
Default Concatenating vcf files

Hi y'all. I'm a retired old guy who spent his whole life wishing that genomics would come along, now it's here and I'm almost too old. But I have some data, a linux system, and some software running, and many problems/questions. Like the oldest dumbest grad student you ever hear of. Very gald to find this site.
Current question is how to concatenate vcf files for individual chromosomes into a single genome. Have been running vcf-concat (from vcf tools) but no matter what I try, get the same error messages.

The column names do not agree in [../Chrm2/Chrm2.vcf].
at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 32
main::error('The column names do not agree in [../Chrm2/Chrm2.vcf].\x{a}') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 114
main::concat('HASH(0x21cf518)') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 12

Yet as near as I can tell, the two .vcf files have exactly the same columns, nice illumina data, looks clean, something just not right. Thanks
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Old 04-07-2012, 12:38 AM   #367
zinky
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Location: china

Join Date: Dec 2011
Posts: 48
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Hi, I am ZHAO, Guangzhou ,China. a student of bioinfromatics engaging in biosoftware developing by Java. recently ,I just focus on RNA-seq data analysis. glad to be here!
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Old 04-09-2012, 06:02 AM   #368
Tahir Mujtaba
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Location: Sweden

Join Date: Mar 2012
Posts: 4
Default Tahir Mujtaba

Hi, I am Tahir from Sweden and i am new to Bioinformatics, i need some help/gudieline to use BOWTIE,TOPHAT,CUFFLINKS, etc, can we negotiate further at ([email protected]).
Quote:
Originally Posted by olus View Post
Hi everibody.
My name is Gabriel, I'm a biologist and bioinformatician. I'm currently working in the core facility of a Molecular Oncology research campus in Milan (italy).
We are using Illumina Genome Analyzer II mainly for ChIP-Seq, but we've already done a resequencing and some RNA-seq are approaching ;-)
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Old 04-09-2012, 06:04 AM   #369
Tahir Mujtaba
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Location: Sweden

Join Date: Mar 2012
Posts: 4
Default

Hello, do you know BOWTIE?,Can you help me learning this tool, i am new to Bioinformatics.
Quote:
Originally Posted by rathankar View Post
dear friends
I am new member for NGS analysis and have the following data. any help would be appreciated from the members or the administrator of the group
1. i am working on mus musculus and in building the indexes, bowtie takes a long time, more than 2 days for all the chromosomes. instead of building the indexes together, which takes a long time for buffering, can i build it one by one?. it takes hardly 25 mins for a single chromosome indexing and hence one can build the indexes for all the chromosomes within 500 mins or less than 10 hrs. pls reply

with regards
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Old 04-09-2012, 10:08 PM   #370
bilalwajidabbas
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Location: College Station, TX

Join Date: Apr 2012
Posts: 1
Default

Dear All,

I am new to the sequencing world and have just managed to install SSAKE and VELVET.
Kindly, tell of how to use them.

Regards
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Old 04-10-2012, 06:54 AM   #371
Maudeulg
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Location: belgium

Join Date: Mar 2012
Posts: 1
Default

Hi,

I am Maude, a phD student in Belgium.
I work on the alternative splicing on the transcriptome using genome analyser (illlumina)

Greetings!
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Old 04-10-2012, 08:46 AM   #372
crazyhottommy
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Location: Gainesville

Join Date: Apr 2012
Posts: 140
Default

Hi !
I am a new bird in next generation seq and data analysis. I am trying to establish the ChIP-seq tech in our lab. I am glad to meet you all here. Thanks for all the helps.

I am a PhD student in the University of Florida, working on cancer metastasis and tumor angiogenesis.
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Old 04-16-2012, 09:52 AM   #373
mukundi
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Location: columbus

Join Date: Apr 2012
Posts: 1
Default hello everyone

i am a bioinformatics masters student workking on my project at ohio state still getting the hang of working and anlysing RNA-seq data
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Old 04-16-2012, 10:09 AM   #374
hylei
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Location: Maryland

Join Date: Dec 2010
Posts: 12
Default

Hi,

My name is Haiyan, a fellow in FDA. We try to identify the new pathogen from the human samples. We will use the Illumina miseq platform. Thanks.

haiyan
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