Question: fastQC for Oxford Nanopore reads
0
gravatar for efratk
10 weeks ago by
efratk0
efratk0 wrote:

Hi,

I want to use fastQC for quality control checks on nanopore sequencing reads. When I ran fastQC it ran a long time without finishing or given an error. I stopped the job after several hours and got an error: "java.lang.OutOfMemoryError: Java heap space" What is the reason for it? Is fastQC good for nanopre reads? (I read that fastQC added support for processing files of Oxford Nanopore reads), Which other tools are recommended for quality control checks on nanopore sequencing reads?

Thanks

sequencing assembly • 409 views
ADD COMMENTlink modified 9 weeks ago • written 10 weeks ago by efratk0

Thanks a lot for the reply

ADD REPLYlink written 9 weeks ago by efratk0
1
gravatar for arfesta
10 weeks ago by
arfesta10
arfesta10 wrote:

Here are a few tools I've used..I think the question comes down to what exactly do you mean by QC (what stats are you trying to find out):

minion_qc

IONiser

Nanoplot..as seen here on biostars

ADD COMMENTlink written 10 weeks ago by arfesta10
0
gravatar for genomax
10 weeks ago by
genomax36k
United States
genomax36k wrote:

See posts #358-359 in this thread for a possible solution.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by genomax36k
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