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Forum: Ion Torrent 06-04-2014, 07:14 PM
Replies: 10
Views: 10,099
Posted By sophiespo
You can try Ion Reporter, it's free to a point. ...

You can try Ion Reporter, it's free to a point.

https://ionreporter.lifetechnologies.com/ir/

I don't think you can just download Torrent Suite, it usually ships with their servers (I could be...
Forum: Introductions 05-07-2014, 08:17 PM
Replies: 3
Views: 1,197
Posted By sophiespo
Maybe you can try some RNA-grade glycogen as a...

Maybe you can try some RNA-grade glycogen as a carrier during precipitation.

If the RNA quality is low but yield is high you can try re-precipitate.
Forum: Bioinformatics 02-06-2014, 05:22 PM
Replies: 6
Views: 19,717
Posted By sophiespo
[/QUOTE] Sorry, this is an old question...

[/QUOTE]


Sorry, this is an old question and it might be solved by now but for anyone who is searching, samtools will print to STDOUT unless you direct it somewhere.


samtools view -H...
Forum: Bioinformatics 12-01-2013, 12:53 AM
Replies: 2
Views: 3,374
Posted By sophiespo
I am currently in the process of validating a...

I am currently in the process of validating a bunch of somatic mutations I detected in some exomes using MuTect and some other algorithms. I've been doing extensive research into the tools available...
Forum: Bioinformatics 10-16-2013, 11:48 PM
Replies: 14
Views: 6,047
Posted By sophiespo
is wrong. It should be:

is wrong.

It should be:
Forum: Bioinformatics 10-14-2013, 08:59 PM
Replies: 3
Views: 3,302
Posted By sophiespo
Can someone please tell me how to achieve this? I...

Can someone please tell me how to achieve this? I use --buildver mm9 and I get this error:

Error in argument: the --buildver argument must be 'hg18' or 'hg19'
Forum: Bioinformatics 10-14-2013, 07:43 PM
Replies: 10
Views: 4,565
Posted By sophiespo
Hello? @dkoboldt

Hello? @dkoboldt
Forum: Introductions 10-01-2013, 06:13 AM
Replies: 2
Views: 1,745
Posted By sophiespo
Just a guess but is the program expecting a...

Just a guess but is the program expecting a tabbed VCF file?
I have had problems when I've had spaces rather than tabs between fields.
Forum: Illumina/Solexa 10-01-2013, 06:08 AM
Replies: 3
Views: 2,753
Posted By sophiespo
JosieSeq I think your problem will be throughput....

JosieSeq I think your problem will be throughput.

I was going to run some Nextera Rapid Capture exomes on the MiSeq but for the coverage we wanted (100X) we would only have been able to run one at...
Forum: Bioinformatics 10-01-2013, 06:00 AM
Replies: 3
Views: 1,854
Posted By sophiespo
If you know what kit was used to enrich your...

If you know what kit was used to enrich your exome then you'll be able to download a BED file from the web. I know that BED files are available for some of the most popular kits (Agilent SureSelect,...
Forum: Bioinformatics 10-01-2013, 05:55 AM
Replies: 10
Views: 4,565
Posted By sophiespo
Hi Dan, I was wondering if you could help...

Hi Dan,

I was wondering if you could help me. I've been trying to get this particular aspect of VarScan2 working for a while.

I am creating my pileup then running VarScan like this:

samtools...
Forum: General 09-23-2013, 04:49 PM
Replies: 2
Views: 3,702
Posted By sophiespo
Sorry to resurrect an old thread but I am also...

Sorry to resurrect an old thread but I am also trying to figure this out.

samtools mpileup -DSuf ref.fa tumor.bam normal.bam | bcftools view -bvcgT pair - > var.bcf

This gives me mutations...
Forum: Bioinformatics 06-20-2013, 06:42 PM
Replies: 4
Views: 3,359
Posted By sophiespo
Thanks for replying. I think I have narrowed down...

Thanks for replying. I think I have narrowed down the problem a little - though I am still not sure what is causing it.

I looked at the file in the command line and excel, looked at my interval...
Forum: Bioinformatics 06-19-2013, 10:50 PM
Replies: 4
Views: 3,359
Posted By sophiespo
ExomeCNV - R - data.frame error

Hi,

I desperately need help.

I have created my coverage file using GATK like the ExomeCNV user guide says.

However when I use read.coverage.gatk("filename") in R, it throws this error:
...
Forum: Bioinformatics 05-15-2013, 02:55 AM
Replies: 22
Views: 12,907
Posted By sophiespo
I am as well when using the...

I am as well when using the somatic/processSomatic functions.

Annovar doesn't like this.. can anyone help?
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