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Search: Posts Made By: qtrinh
Forum: Bioinformatics 10-11-2012, 05:40 AM
Replies: 7
Views: 3,971
Posted By qtrinh
Hi, If there are enough interests on a user...

Hi,
If there are enough interests on a user guide on how to get starting with Amazon EC2, I can put one together.

Q
Forum: Bioinformatics 10-11-2012, 05:36 AM
Replies: 7
Views: 3,971
Posted By qtrinh
Hi, You can use the "High-Memory Quadruple...

Hi,
You can use the "High-Memory Quadruple Extra Large Instance" instance type, which comes with 64GB of RAM and costs $1.8 per hour:
http://aws.amazon.com/ec2/instance-types/

For...
Forum: Bioinformatics 10-11-2012, 05:04 AM
Replies: 6
Views: 4,247
Posted By qtrinh
Hi, You can also try IDR: ...

Hi,
You can also try IDR:

https://sites.google.com/site/anshulkundaje/projects/idr

Q
Forum: Bioinformatics 10-09-2012, 11:59 AM
Replies: 4
Views: 1,319
Posted By qtrinh
Hi, You should be able to use samtools to...

Hi,
You should be able to use samtools to split your bam file into multiple bam files.
Here is how:

# get the list of all sample names in INPUT.bam
> samtools view -H INPUT.bam | awk '$0 ~...
Forum: Bioinformatics 10-05-2012, 02:38 AM
Replies: 8
Views: 2,464
Posted By qtrinh
Hi, What about running RealignerTargetCreator...

Hi,
What about running RealignerTargetCreator in parallel on each of the chromosomes ? This should speed things up for you.

Q
Forum: Bioinformatics 10-05-2012, 02:31 AM
Replies: 3
Views: 4,923
Posted By qtrinh
Hi, You are missing the boost library. ...

Hi,
You are missing the boost library. Install the boost library and try again. Here are my notes from a while back:

# install dependencies
sudo yum update
sudo yum install gcc-c++.x86_64...
Forum: Bioinformatics 01-12-2012, 03:04 AM
Replies: 2
Views: 1,132
Posted By qtrinh
You can use samtools to do this. i.e., samtools...

You can use samtools to do this. i.e., samtools faidx REGION
Forum: Bioinformatics 08-19-2011, 04:16 AM
Replies: 26
Views: 17,080
Posted By qtrinh
ninad, I think the issue started with your...

ninad,
I think the issue started with your cat step. Try putting your hg19s.fa in another directory.

~/chromFa$ mkdir hg19
~/chromFa$ cat *.fa >hg19/hg19s.fa
~/chromFa$ bwa index -a bwtsw...
Forum: Bioinformatics 06-29-2011, 01:01 PM
Replies: 7
Views: 2,163
Posted By qtrinh
I did the A,C,G,T, and N frequencies analysis a...

I did the A,C,G,T, and N frequencies analysis a while back and for the 3 gigabases human reference genome including random and unknown, I get:

A 27.25%
C 18.9%
G 18.9%
T 27.28%
N 7.64%
...
Forum: Bioinformatics 04-19-2011, 01:22 PM
Replies: 20
Views: 16,913
Posted By qtrinh
Did you use 'danRer6.fa' in your alignment step?...

Did you use 'danRer6.fa' in your alignment step? I think the issue here is that the reference used in the alignment step is not the same as 'danRer6.fa'
Forum: Bioinformatics 04-05-2011, 09:25 AM
Replies: 1
Views: 2,096
Posted By qtrinh
you can extract these DNA regions from build 36...

you can extract these DNA regions from build 36 with some flanking then use blat or blast to find their coordinates in build 37.

Q
Forum: Bioinformatics 09-08-2010, 06:36 PM
Replies: 1
Views: 2,702
Posted By qtrinh
Here is a link that describes the output of...

Here is a link that describes the output of consensus and indels calling: http://samtools.sourceforge.net/cns0.shtml
Forum: Bioinformatics 05-14-2010, 06:51 AM
Replies: 11
Views: 3,121
Posted By qtrinh
Yes, that's what we did (i.e., downloaded the...

Yes, that's what we did (i.e., downloaded the source and followed the build instructions). It's not too bad ...
Forum: Bioinformatics 05-14-2010, 06:28 AM
Replies: 11
Views: 3,121
Posted By qtrinh
You can also download the UCSC and install it...

You can also download the UCSC and install it locally on a dedicated server. Loading large data sets will be much faster.

Q
Forum: Bioinformatics 03-25-2009, 11:58 AM
Replies: 292
Views: 151,909
Posted By qtrinh
Hi Heng, I did do "samtools sort" first. ...

Hi Heng,
I did do "samtools sort" first. Here is what I did:

samtools import homo_sapiens.fasta.fai S1.sam S1.bam

samtools sort S1.bam S1_sorted

samtools pileup -f homo_sapiens.fasta -c...
Forum: Bioinformatics 03-25-2009, 11:43 AM
Replies: 292
Views: 151,909
Posted By qtrinh
I got seg fault when doing "samtools pileup". ...

I got seg fault when doing "samtools pileup". The error message is "[bam_pileup_core] the input is not sorted. Abort!", however I do use the sorted input file. Anyone else seen this before?

Q
Forum: Illumina/Solexa 03-19-2009, 08:00 AM
Replies: 8
Views: 4,503
Posted By qtrinh
Yes, I agree with westerman, Perl is also good. ...

Yes, I agree with westerman, Perl is also good. I found myself using a bit of Perl, awk, and sed everyday.

Q
Forum: Illumina/Solexa 03-18-2009, 07:56 AM
Replies: 8
Views: 4,503
Posted By qtrinh
cat MAQ_SNP_FILE | awk '{ if (($4!="A") &&...

cat MAQ_SNP_FILE | awk '{ if (($4!="A") && ($4!="C") && ($4!="G") && ($4!="T") ) { print $0 } }' > het.snps



cat MAQ_SNP_FILE | awk '{ if (($4=="A") || ($4=="C") || ($4=="G") || ($4=="T") ) {...
Forum: Illumina/Solexa 03-18-2009, 06:47 AM
Replies: 8
Views: 4,503
Posted By qtrinh
No ... no ... no perl ... a one-liner bash with...

No ... no ... no perl ... a one-liner bash with awk will do. Let me know if you need the one-liner ... :-)

Q
Forum: Illumina/Solexa 03-13-2009, 04:37 AM
Replies: 8
Views: 4,503
Posted By qtrinh
Hi, Running the command 'maq cns2snp in.cns >...

Hi,
Running the command 'maq cns2snp in.cns > out.snp' should give you the info you are looking for - see http://maq.sourceforge.net/maq-manpage.shtml for output column descriptions.

Q
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