[oliviajm]

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.

[rathankar]

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

[tusharbiot]

Hi to all

I am a doctoral student, assembling partial fosmid libraries and organellar genome from the plant family Zingiberaceae.

[Virology]

Hi everybody
I am a virology graduate student, preparing to do a whole genome sequence project using 454.
Good luck!

[wesserg]

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).

[AllanLindh]

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

[zinky]

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!

[Tahir Mujtaba]

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]).

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 ;-)

[Tahir Mujtaba]

Hello, do you know BOWTIE?,Can you help me learning this tool, i am new to Bioinformatics.

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

[bilalwajidabbas]

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

[Maudeulg]

Hi,

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

Greetings!

[crazyhottommy]

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.

[mukundi]

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

[hylei]

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