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Forum: MGISEQ (FKA Complete Genomics) 10-22-2014, 07:03 AM
Replies: 0
Views: 3,685
Posted By Firebird
Annotation of Genomes

Hi,

I have expierence with exome annotaion, which is quite simple as you are only looking into coding sequences. That make interpretation of the results much easier.
But how do I annotate the...
Forum: Bioinformatics 06-20-2011, 12:32 AM
Replies: 9
Views: 1,851
Posted By Firebird
Hi, thanks for the ideas. I used the...

Hi,

thanks for the ideas.

I used the "view" command to have a look at the .bam file. It is written that it was alignt with a file called "chr1.fa". Therefore I changed my reference file to...
Forum: Bioinformatics 06-17-2011, 07:05 AM
Replies: 9
Views: 1,851
Posted By Firebird
N in pileup file

Hi,

I have sequence-information generated on a illumina sequencer. The aligment was done with ELAND and the output is a .bam file.

Now I wanted to generate a pileup-file with the mpileup...
Forum: Bioinformatics 01-19-2011, 06:57 AM
Replies: 6
Views: 1,319
Posted By Firebird
@doc.ramses: I tried it with Excel, but I'll...

@doc.ramses: I tried it with Excel, but I'll check out Acess.

@colindaven: I also use galaxy, nice website btw. Which feature can I use for intersection. Can you may tell me the workflow?

Thanks
Forum: Bioinformatics 01-18-2011, 05:30 AM
Replies: 6
Views: 1,319
Posted By Firebird
I am not good either in R or in Python. Is there...

I am not good either in R or in Python. Is there maybe a command line tool I can use? My data is in .tab format.

Thank you
Forum: Bioinformatics 01-11-2011, 05:50 AM
Replies: 6
Views: 1,319
Posted By Firebird
Intersection

Hello,

I want to do an intersection of several exomes to find common mutations in these exomes. How can I do that?

Thanks
Forum: Bioinformatics 12-17-2010, 05:55 AM
Replies: 8
Views: 2,576
Posted By Firebird
No, unfortunatly I'm not familiar with R. I...

No, unfortunatly I'm not familiar with R.

I can try it with the code u provided. Is it ok when I just change the path to my file?

Thank
Forum: Bioinformatics 12-17-2010, 01:01 AM
Replies: 8
Views: 2,576
Posted By Firebird
Show Overall Coverage

Hi,

is there a possibility to get an overview picture of the coverage? I can do this with IGV only for parts of a chromosome when I am zoomed in very deep.

Further more, is there a possiblity...
Forum: Literature Watch 12-02-2010, 07:04 AM
Replies: 1
Views: 1,740
Posted By Firebird
Is there a possibility to access these data in...

Is there a possibility to access these data in the same way it is possible with the 1000 genomes data.
Forum: Bioinformatics 12-02-2010, 03:53 AM
Replies: 11
Views: 1,466
Posted By Firebird
I have the same problem. Is there a link to get...

I have the same problem.
Is there a link to get the full hg19 directly, withouth assembling it from all chromosomes?
I also use Ubuntu on a 32 bit machine.
Forum: Bioinformatics 08-13-2010, 05:39 AM
Replies: 27
Views: 6,191
Posted By Firebird
Can you please tell me how many individuals are...

Can you please tell me how many individuals are included in the last release?

So with this approach you are only able to call common variants? But isn't it a goal of the project to detect variants...
Forum: Bioinformatics 08-13-2010, 03:22 AM
Replies: 27
Views: 6,191
Posted By Firebird
Did you also call variants from this 653 samples?...

Did you also call variants from this 653 samples?

Btw. I have a question about you called variants in the pilot 1 study. Did I undestand it right, that you pooled all the low coverage sequence...
Forum: Bioinformatics 08-13-2010, 01:37 AM
Replies: 27
Views: 6,191
Posted By Firebird
Hello, how can I access the data from the...

Hello,

how can I access the data from the 2000 Individuals sequenced with a 4 x coverage.

Thanks
Forum: Bioinformatics 08-04-2010, 11:55 AM
Replies: 27
Views: 6,191
Posted By Firebird
@BetterPrimate I was also looking for an...

@BetterPrimate

I was also looking for an overall VCF file, but I could only find genotypes per population per pilot study.

An overall files for the whole project would be fine.
Forum: Bioinformatics 06-16-2010, 10:48 PM
Replies: 3
Views: 1,172
Posted By Firebird
Thank you, but can you tell me the synthax for...

Thank you, but can you tell me the synthax for "grep".
Forum: Bioinformatics 06-16-2010, 06:44 AM
Replies: 27
Views: 6,191
Posted By Firebird
1000 Genomes Data/ Exon targetted

Hi,

I have a question concerning the 1000 Genomes Data. On the ftp they have lowcoverage and exontargetted data.
I assume that the exontagetted files only contain sequence information of the...
Forum: Bioinformatics 06-16-2010, 06:37 AM
Replies: 3
Views: 1,172
Posted By Firebird
Samtools comand problem

Hi,

I have a problem with the comand "view".
I only want to view 1 nukleotide, but when I write something like 1:100-100 I always get more than 1 base.

Is there an option for the "pileup"...
Forum: Bioinformatics 06-14-2010, 10:39 PM
Replies: 11
Views: 4,804
Posted By Firebird
Hello, I want to do the same like...

Hello,

I want to do the same like michelle.lupton with SNPs I found. I used the samtools and the view comand.
My problem is that I need an automated function to check all data from all...
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