Question: fastQC for Oxford Nanopore reads
0
gravatar for efratk
16 days 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 • 210 views
ADD COMMENTlink modified 11 days ago • written 16 days ago by efratk0

Thanks a lot for the reply

ADD REPLYlink written 11 days ago by efratk0
1
gravatar for arfesta
16 days 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 16 days ago by arfesta10
0
gravatar for genomax
16 days ago by
genomax33k
United States
genomax33k wrote:

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

ADD COMMENTlink modified 16 days ago • written 16 days ago by genomax33k
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