2 hours ago by
Does fastq-dump return interleaved files?
For example,
fastq-dump ERR315863
Here's the head of my file:
(base) -bash-4.1$ head -n 10 ERR315863.fastq
@ERR315863.1 MERCURE:0070:0:8:1:3672:2101 length=94
AACCCCAACCTCCAAGCCCTCTTCAACGATCCCACCACCCTCAATTGGCATAGGTCAGTTTTTTTTTCGGTGCCGGTGAGGAGGCCTAGCTGGC
+ERR315863.1 MERCURE:0070:0:8:1:3672:2101 length=94
[email protected]?DE;[email protected]*ED8><)<<;CDEC=EBC/8CDA.DC58579;C//BDB/CDA<@<:=19722),:;<[email protected]@
@ERR315863.2 MERCURE:0070:0:8:1:3733:2124 length=186
AAAAGTGATGATCGCGCTAATTTCTTAAGTAAACTTATGAGAATTACACAAAATGTAAAATTTGACATTTATGGAATTCAAAAGCTAAGATTTAGTCCCATTTTAGAGTTAGATATAGCTTTGAAATAATGATCTGCCCATATTGGTTGAATATTTTGAATTCCATAAATGTCAAGTTTTACATTT
+ERR315863.2 MERCURE:0070:0:8:1:3733:2124 length=186
[email protected]@DADDEEFFCE6EE/[email protected]/D/.>*,;>8A4:59>A>?+5>A>:>)[email protected];FGHCAD.C,@BC=DBBFFB6BD?EEBE8/*[email protected]@EEEEEFHHEADFF;[email protected]?:8.>:[email protected];,75.>=6=-<9DEA
@ERR315863.3 MERCURE:0070:0:8:1:3611:2223 length=155
GAGTGATCCTGGGATACTCAATAAATATGATCTCAGTTCTCATAAAGTAGCTATTCATGCTGCGGCGACCGTGAGGAGGTAAGCACTCATCAGGGGGGCAGGCGGGGAACCCATTGAATTCAGTTCCAGCATAATATTCATGAATAATTGGCCAC
This run is HiSeq 2000 so I'm assuming it's R1/R2 reads but these reads don't look paired:
www.ebi.ac.uk/metagenomics/runs/ERR315863
What did fastq-dump download with this command and not specifying --split-files?
