Difference between revisions of "Petagene"
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# Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/) | # Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/) | ||
| − | == | + | == 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 | ||
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</syntaxhighlight> | </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). | + | 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/ | 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: | 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> |
| + | 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) | + | 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). |
Latest revision as of 14:34, 23 November 2015
Petagene install
- 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)
- Unpack corpus.tar.gz to some path (e.g. /var/genecodeq/)
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.gzYou'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.bamIn 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).