Question: fastq-dump split-3 output
3
gravatar for colonppg
3.6 years ago by
colonppg100
United States
colonppg100 wrote:

If I run fastq-dump split-3 on a sra file, I got

file_1.fastq

file_2.fastq

file.fastq

My questions is how I handle file.fastq? Should I just ignore it?

 

fastq-dump sra • 7.1k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by colonppg100
8
gravatar for osullivanchristopher
3.6 years ago by
United States
osullivanchristopher180 wrote:

--split-3 will output 1,2, or 3 files: 1 file means the data is not paired. 2 files means paired data with no low quality reads or reads shorter than 20bp. 3 files means paired data, but asymmetric quality or trimming.  in the case of 3 file output, most people ignore <file>.fastq . this is a very old formatting option introduced for phase1 of 1000genomes.  before there were many analysis or trimming utilities and SRA submissions  always contained all reads from sequencer. back then nobody wanted to throw anything away. you might want to use --split-files instead. that will give only 2 files for paired-end data. or not bother with text output and access the data directly using sra ngs apis.

ADD COMMENTlink written 3.6 years ago by osullivanchristopher180

On some occasions with "--split-files", you have to use "-M 0" or else end up with unpaired reads, due to fastq-dump discarding small reads but keeping its pair.

ADD REPLYlink written 3.6 years ago by h.mon24k
2
gravatar for Devon Ryan
3.6 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Generally file.fastq is much smaller than the other two and the result of orphaned reads after trimming. I would typically ignore that file unless you really need the extra reads. The exception is if file.fastq is larger than either of the other two fastq files. In that case, you probably want to ignore the paired-end reads (or just use them to get things like the insert size distribution).
 

ADD COMMENTlink written 3.6 years ago by Devon Ryan89k
0
gravatar for colonppg
3.6 years ago by
colonppg100
United States
colonppg100 wrote:

Thanks so much! guys!

ADD COMMENTlink written 3.6 years ago by colonppg100
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