Question: Storing Fastq As Unaligned Bam
2
gravatar for Abhi
7.1 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

Hey Guys

Just wondering if anyone there is now storing the raw fastq data as unaligned bam files. We are reaching a stage where any space we could potentially save would be beneficial.

Any con of storing fastq as bam ? I see some discussion about this on seqanswers : http://seqanswers.com/forums/showthread.php?t=14941

Also any tools that people already have that converts a fastq to bam and vice-a-versa. I know there are few which can do bam to fastq like picard but not sure if fastq to bam is there.

Thanks! -Abhi

fastq bam • 6.3k views
ADD COMMENTlink written 7.1 years ago by Abhi1.5k

This doesn't read like a stackexcahnge question to me - if you want a discussion why not continue on SEQanswers?

ADD REPLYlink written 7.1 years ago by Peter5.7k

This seems relevant to me, handling large NGS data files is an increasing bioinformatic issue.

ADD REPLYlink written 7.1 years ago by Ian5.3k
2
gravatar for Pierre Lindenbaum
7.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

I think a bgzipped fastq file will be always smaller than a BAM file as the BAM file also contains the positions of the alignments.

See also:

http://bioinformatics.oxfordjournals.org/content/early/2011/01/19/bioinformatics.btr014.abstract

Compression of genomic sequences in FASTQ format

and

http://genome.cshlp.org/content/early/2011/01/18/gr.114819.110

Efficient storage of high throughput sequencing data using reference-based compression

ADD COMMENTlink written 7.1 years ago by Pierre Lindenbaum114k
1
gravatar for toni
7.1 years ago by
toni2.1k
Lyon
toni2.1k wrote:

Hi Abhi,

yes we do this in our team. You can use Picard 'FastqToSam' utility.

Compared to 2 fastq files (plain, not gzipped as suggested by Pierre), an unaligned BAM file allows to save 60°% to 65% of storage space. It is also practical because you can store some useful information (Sample, Library, Run, any useful comments ...) in the header if you want to.

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by toni2.1k
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