Question

IONizeR writeFastq function

0

Entering edit mode

playerraa • 0

@playerraa-10987

Last seen 7.8 years ago

Trying to writeFastq with IONizeR package but the written file is in binary!

How can I get a human readable fastq from a fast5 using IONizer?

Also, a different program would be just as well, though I'd rather be able to stick with IONizeR.

Lookin' at you Mike Smith! ;)

Thanks,

Rob

IONizeR MinION fast5 • 792 views

ADD COMMENT • link updated 7.8 years ago by Martin Morgan 25k • written 7.8 years ago by playerraa • 0

score 1 · Answer 1 · 2016-06-27

1

Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 3 days ago

United States

The file is compressed by default. Lookin' at the help page ?writeFastq indicates that there is an argument compress, set it to FALSE

writeFastq(obj, compress=FALSE)

ADD COMMENT • link 7.8 years ago Martin Morgan 25k

0

Entering edit mode

Thank you Martin, I'll continue to make investigating the help pages second nature!

Amazing what you can find in the help docs... haha.

It also did not cross my mind that it was just gz compressed. Since it has you name your own output it wasn't obvious what encoding was being used.

ADD REPLY • link 7.8 years ago playerraa • 0