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Forum: RNA Sequencing 10-18-2013, 04:34 AM
Replies: 1
Views: 1,419
Posted By nexgengirl
RNAseq Genes Different By File

Hi,

I have diff files from ~20 different RNA sequencing experiments. A common GTF file was utilized to make these diff files. The number and identity of the genes in the diff files is different...
Forum: Bioinformatics 04-16-2013, 01:51 PM
Replies: 6
Views: 1,996
Posted By nexgengirl
See Bukowski answer. It came up as I was entering...

See Bukowski answer. It came up as I was entering the previous post.
Forum: Bioinformatics 04-16-2013, 01:49 PM
Replies: 6
Views: 1,996
Posted By nexgengirl
I have not personally used the Haloplex platform...

I have not personally used the Haloplex platform before. I've analyzed a lot of exome data but not Haloplex.

From briefly looking at the information on the Agilent site it seems that first the DNA...
Forum: Bioinformatics 04-16-2013, 11:40 AM
Replies: 6
Views: 1,996
Posted By nexgengirl
How was the DNA prepared? Was it hybridization or...

How was the DNA prepared? Was it hybridization or pcr based design? If it was PCR-based you would expect high PCR duplication rate but if it was hybridization based then yes this is high.
Forum: Academic/Non-Profit Jobs 02-28-2013, 03:09 PM
Replies: 0
Views: 1,930
Posted By nexgengirl
Research Data Analyst: Johns Hopkins University School of Medicine

General Summary: Work in collaboration with scientists and trainees in a human genetics laboratory to address research questions involving the genomic study of complex human disease. The candidate...
Forum: Bioinformatics 02-20-2013, 05:15 PM
Replies: 8
Views: 3,738
Posted By nexgengirl
Picard's hybridization statistics tool could be...

Picard's hybridization statistics tool could be used. Description at the link below:

http://picard.sourceforge.net/command-line-overview.shtml#CalculateHsMetrics
Forum: Bioinformatics 12-13-2012, 04:09 PM
Replies: 4
Views: 1,907
Posted By nexgengirl
Hi all, Thanks for your suggestions. I...

Hi all,

Thanks for your suggestions. I reran the bwa sampe with the -A option to get it to run. It ran successfully in 16 minutes!

Thanks again.
Forum: Bioinformatics 12-11-2012, 03:36 PM
Replies: 4
Views: 1,907
Posted By nexgengirl
Remapping 1000 Genomes Data with BWA

Hi,

I'm working now to remap some 1000 genomes exome data with BWA to compare with other exomes I've aligned with BWA. These were originally mapped with Mosaik. I've hit a bit of a snag and I'm...
Forum: General 12-11-2012, 07:22 AM
Replies: 3
Views: 1,635
Posted By nexgengirl
Check out the readLines function in R.

Check out the readLines function in R.
Forum: Genomic Resequencing 11-21-2012, 05:01 AM
Replies: 6
Views: 2,544
Posted By nexgengirl
Check out section 6 on this page: ...

Check out section 6 on this page:

http://gatkforums.broadinstitute.org/discussion/1237/using-the-unified-genotyper

It explains how the genotypes on the sex chromosomes are called in GATK
Forum: Bioinformatics 11-14-2012, 04:51 AM
Replies: 1
Views: 1,709
Posted By nexgengirl
Check out the 1000 genomes ftp. They have raw...

Check out the 1000 genomes ftp. They have raw exome (fastq) as well as aligned exome (bam) data. Here's the link to the index of fastq files:
...
Forum: Bioinformatics 09-08-2012, 10:30 AM
Replies: 11
Views: 11,898
Posted By nexgengirl
Since showing the file on here doesn't look so...

Since showing the file on here doesn't look so good I have also attached the first 130 lines as a file so you can see how it looks in the terminal.
Forum: Bioinformatics 09-08-2012, 10:24 AM
Replies: 11
Views: 11,898
Posted By nexgengirl
Yes, I did get this to work. The file is too...

Yes, I did get this to work. The file is too large to attach so I'll show the header of the file below.

Here's the command I used:

java -Xmx10g -jar...
Forum: Bioinformatics 08-21-2012, 08:28 AM
Replies: 5
Views: 4,404
Posted By nexgengirl
GATK now has a patch for this: ...

GATK now has a patch for this:

http://gatkforums.broadinstitute.org/discussion/1358/solid-read-color#latest
Forum: Sample Prep / Library Generation 07-02-2012, 05:55 PM
Replies: 2
Views: 2,087
Posted By nexgengirl
We've had success with the 96 Well PureLink Pro...

We've had success with the 96 Well PureLink Pro kit from Invitrogen

http://products.invitrogen.com/ivgn/product/K310096A

Hope this helps.
Forum: 454 Pyrosequencing 05-16-2012, 05:05 PM
Replies: 12
Views: 5,309
Posted By nexgengirl
You can also skip using the sizing solution....

You can also skip using the sizing solution. Check out the attached paper for further details on amplicon sequencing with 454 junior and ligating adaptors
Forum: Bioinformatics 05-16-2012, 04:57 PM
Replies: 12
Views: 2,758
Posted By nexgengirl
Hi struggler, I agree with GenoMax. Try and...

Hi struggler,

I agree with GenoMax. Try and install these tools. Otherwise, if you are concerned about that maasha's suggestion of Galaxy is also good. They have a tool there under Fetch sequences...
Forum: Bioinformatics 05-16-2012, 04:19 AM
Replies: 12
Views: 2,758
Posted By nexgengirl
You could also use bedtools...

You could also use bedtools (code.google.com/p/bedtools/). I've used this tool to extract sub-sequence data before and I really like it because its fast and efficient.

The tool in bedtools is...
Forum: Bioinformatics 03-28-2012, 07:05 PM
Replies: 4
Views: 2,263
Posted By nexgengirl
Check out this tool: ...

Check out this tool:

http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq

It will convert a sam or a bam to a fastq. That would get you at least half way to a fasta file.
...
Forum: Bioinformatics 03-20-2012, 04:25 AM
Replies: 13
Views: 4,454
Posted By nexgengirl
Yes, the broad ftp is good or here as well: ...

Yes, the broad ftp is good or here as well:

ftp://ftp.sanger.ac.uk/pub/1000genomes/tk2/main_project_reference/
Forum: Bioinformatics 03-07-2012, 09:27 PM
Replies: 9
Views: 10,924
Posted By nexgengirl
Also, if you want to loop through many bam files...

Also, if you want to loop through many bam files which are in the same directory you could use this command:

for i in *bam
do
java -jar -Xmx10g...
Forum: Bioinformatics 03-07-2012, 09:04 PM
Replies: 9
Views: 10,924
Posted By nexgengirl
I think you will want to look at picard tools...

I think you will want to look at picard tools (http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups) to fix this problem.

Below I've listed an example of how I've used...
Forum: Bioinformatics 12-03-2011, 08:23 AM
Replies: 8
Views: 3,926
Posted By nexgengirl
Thanks Chipper and nilshomer! I reran using the...

Thanks Chipper and nilshomer! I reran using the new version and now there are no reads failing this filter: MappingQualityUnavailableFilter

It seems to be working much better now.

Thanks again.
Forum: Bioinformatics 11-29-2011, 07:08 PM
Replies: 8
Views: 3,926
Posted By nexgengirl
I will try again using the new version (0.7.0a)....

I will try again using the new version (0.7.0a). Before I used 0.6.5a. My only concern is that the manual for the new version on page 39 also says "If a read has one alignment, then the mapping...
Forum: Bioinformatics 11-29-2011, 09:47 AM
Replies: 8
Views: 3,926
Posted By nexgengirl
Thanks Chipper. If I may ask what did you...

Thanks Chipper.

If I may ask what did you find was an appropriate change for the mapping quality? Could it merely be changed to 254 or is it more complex than that? Thanks again.
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