I was trying to convert a cram file to two paired end fastq.gz files using the samtools command:
samtools fastq -c -@2 -1 Sample_R1.fastq.gz -2 Sample_R2.fastq.gz Sample.cram
I'm not sure if I am giving the right command for compression, since the .gz file is huge. Does this command look ok?
thanks!
•
written
by
bsmith030465
file Sample_R1.fastq.gz
Sample_R1.fastq.gz: gzip compressed data, from Unix, max speed
genomax is right, you have to use the right number as compression level to samtools fastq using -c option
In samtools fastq -c option accepts compression level starting from 0 to 9.
Here 0 means fastest but poor compression whereas 9 indicates slowest but best compression.
So you just need to provide the right number for compression level.
As discussed here, you can use -c 6 (gzip default compression level is 6).
So command will be,
samtools fastq -c 6 -@2 -1 Sample_R1.fastq.gz -2 Sample_R2.fastq.gz Sample.cram
Log in to answer this question.
