Marijuana assembly: Difference between revisions
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cat *_1_sequence* > R1_all.fastq.gz & | cat *_1_sequence* > R1_all.fastq.gz & | ||
cat *_2_sequence* > R2_all.fastq.gz & | cat *_2_sequence* > R2_all.fastq.gz & | ||
== Convert files == | |||
Using seqret from EMBOSS. If fresh install, don't forget "sudo ldconfig" to load libraries. | |||
zcat R1_all.fastq.gz | seqret fastq-sanger::stdin fastq-illumina::stdout | gzip > R1_converted.fastq.gz | |||
zcat R2_all.fastq.gz | seqret fastq-sanger::stdin fastq-illumina::stdout | gzip > R2_converted.fastq.gz | |||
Latest revision as of 16:13, 20 August 2011
Obtain raw reads
Sequences obtained from: http://csativa.elasticbeanstalk.com/
Info:
The sequence data is derived from an ILMN HiSeq v2.0 chemistry with 2x100 reads. There are 7 Lanes in total which add up to 131Gb of sequence. The genome is estimated to be 400Mb thus an estimated 327X coverage.
Merge read files
cat *_1_sequence* > R1_all.fastq.gz & cat *_2_sequence* > R2_all.fastq.gz &
Convert files
Using seqret from EMBOSS. If fresh install, don't forget "sudo ldconfig" to load libraries.
zcat R1_all.fastq.gz | seqret fastq-sanger::stdin fastq-illumina::stdout | gzip > R1_converted.fastq.gz zcat R2_all.fastq.gz | seqret fastq-sanger::stdin fastq-illumina::stdout | gzip > R2_converted.fastq.gz