Petagene - Revision history

Michael: /* petagene Use */

2015-11-23T14:34:51Z

petagene Use

Michael: /* petagene Use */

2015-11-23T14:34:08Z

petagene Use

Michael: /* petagene Use */

2015-11-23T14:32:37Z

petagene Use

Michael: /* Petagene install */

2015-11-23T14:31:55Z

Petagene install

Michael: Created page with "== Petagene install == 1) Download the binary 2) Download corpus.tar.gz from the following page: http://www.petagene.com/eval/genecodeq/ (please note that this is a 21GiB fi..."

2015-11-23T14:31:29Z

Created page with "== Petagene install == 1) Download the binary 2) Download corpus.tar.gz from the following page: http://www.petagene.com/eval/genecodeq/ (please note that this is a 21GiB fi..."

New page

== Petagene install ==

1) Download the binary
2) Download corpus.tar.gz from the following page: http://www.petagene.com/eval/genecodeq/ (please note that this is a 21GiB file)
3) Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/)

== petagene Use ==

Using GeneCodeq for FASTQ files:

One can compress FASTQ input files (e.g. in.fastq.gz) in the following way:
> genecodeq.1.0.1.centos6 -r /var/genecodeq/hs37d5.seq -v /var/genecodeq/1kGenomeProjectT16.vcf -i in.fastq.gz -o out.fastq.gz

You'll notice from above, that this takes a compressed fastq file (i.e. in.fastq.gz) and produces another compressed fastq file (i.e. out.fastq.gz).

Using GeneCodeq for BAM files:

One needs to install samtools in order to use GeneCodeq with BAM files. The systems that your client uses should most likely have this already installed. If they don't, it can be downloaded from http://www.htslib.org/download/

Once samtools is installed, you can use GeneCodeq to compress BAM files (e.g. in.bam) in the following way:
> samtools view -h in.bam | genecodeq.1.0.1.centos6 -r /var/genecodeq/hs37d5.seq -v /var/genecodeq/1kGenomeProjectT16.vcf -t SAM | samtools view -b - -o out.bam

In both cases (FASTQ or BAM), you should see a considerable difference in file sizes (e.g. in.fastq.gz vs out.fastq.gz and in.bam vs out.bam). As I said before, please share any performance numbers you gather with us.

@@ Line 5: / Line 5: @@
 # Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/)
-== petagene Use ==
+== Using GeneCodeq for FASTQ files ==
 One can compress FASTQ input files (e.g. in.fastq.gz) in the following way
@@ Line 14: / Line 14: @@
 </syntaxhighlight>
 You'll notice from above, that this takes a compressed fastq file (i.e. in.fastq.gz) and produces another compressed fastq file (i.e. out.fastq.gz).
-−
 ==Using GeneCodeq for BAM files==

@@ Line 16: / Line 16: @@
 You'll notice from above, that this takes a compressed fastq file (i.e. in.fastq.gz) and produces another compressed fastq file (i.e. out.fastq.gz).
-Using GeneCodeq for BAM files:
+==Using GeneCodeq for BAM files==
 One needs to install samtools in order to use GeneCodeq with BAM files. The systems that your client uses should most likely have this already installed. If they don't, it can be downloaded from http://www.htslib.org/download/
 Once samtools is installed, you can use GeneCodeq to compress BAM files (e.g. in.bam) in the following way:
-> samtools view -h in.bam | genecodeq.1.0.1.centos6 -r /var/genecodeq/hs37d5.seq -v /var/genecodeq/1kGenomeProjectT16.vcf -t SAM | samtools view -b - -o out.bam
+<syntaxhighlight>
-In both cases (FASTQ or BAM), you should see a considerable difference in file sizes (e.g. in.fastq.gz vs out.fastq.gz and in.bam vs out.bam). As I said before, please share any performance numbers you gather with us.
+In both cases (FASTQ or BAM), you should see a considerable difference in file sizes (e.g. in.fastq.gz vs out.fastq.gz and in.bam vs out.bam).

@@ Line 9: / Line 9: @@
 Using GeneCodeq for FASTQ files:
-One can compress FASTQ input files (e.g. in.fastq.gz) in the following way:
+One can compress FASTQ input files (e.g. in.fastq.gz) in the following way
-> genecodeq.1.0.1.centos6 -r /var/genecodeq/hs37d5.seq -v /var/genecodeq/1kGenomeProjectT16.vcf -i in.fastq.gz -o out.fastq.gz
+<syntaxhighlight>
 genecodeq.1.0.1.centos6 -r /var/genecodeq/hs37d5.seq -v /var/genecodeq/1kGenomeProjectT16.vcf -i in.fastq.gz -o out.fastq.gz
 You'll notice from above, that this takes a compressed fastq file (i.e. in.fastq.gz) and produces another compressed fastq file (i.e. out.fastq.gz).

@@ Line 1: / Line 1: @@
 == Petagene install ==
-) Download the  binary
+# Download the  binary
-) Download corpus.tar.gz from the following page: http://www.petagene.com/eval/genecodeq/ (please note that this is a 21GiB file)
+# Download corpus.tar.gz from the following page: http://www.petagene.com/eval/genecodeq/ (please note that this is a 21GiB file)
-) Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/)
+# Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/)
 == petagene Use ==