Question: understanding the output files of fasterq-dump --split-files
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gravatar for inbal.tzipermanl
23 months ago by
inbal.tzipermanl0 wrote:

I am using fasterq-dump to download from sra, and using split-files to split paired end reads. as a result i receive one or two files. when i have two files they are in the format *_1.fastq, and another file *_2.fastq or *_3.fastq or *_4.fastq I cannot find what is the meaning of these numbers?

the command I am using: fasterq-dump --split-files -O /media/lab/fastq ERR016705

for example: ERR016705 has 2 files: _1, _4 ERR015587 has 2 files: _1, _2

fasterq-dump • 2.0k views
ADD COMMENTlink modified 23 months ago by genomax85k • written 23 months ago by inbal.tzipermanl0
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gravatar for genomax
23 months ago by
genomax85k
United States
genomax85k wrote:

Have you looked at the headers of the fastq files. Even though the files themselves are named 1 and 4 the headers should tell you that these are R1 and R2 files.
(Note: Illumina sequencing happens in Read 1 --> Index 1 --> Index 2 --> Read 2 order. Sometimes people may dump index sequences into individual files and in that case output files have File 1 --> File 2 --> File 3 --> File 4 names.)

ADD COMMENTlink modified 23 months ago • written 23 months ago by genomax85k
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