Entering edit mode
7 months ago
machaalani29
•
0
hello, so I have some WGS data, and I was given the cram and cram.crai; I want to change them to fastq I am using samtools:
samtools fastq -O -c 7 C-7507T.cram > C-7507T.fastq.gz
The cram file is 32G The fastq file is 583G
is that difference in size normal?
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alignments did not result in duplicate reads entries.
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
I am 99.99 sure that your fastq file is not compressed. What is
file C-7507T.fastq.gz
? I do not think samtools autodetects suffix if you send to stdout like that.the option -c is to compress the file
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a
head
of the fastq file and see whether it is text or binary.