gringer / bioinfscripts Goto Github PK

Hi David, the Oxford Nanopore site is pointing to your bioinfscripts as the location for the fast5extactor.py script but I can't seem to find it- did it get moved somewhere else?
thanks! -Scott

Hey, I am running into errors when executing the following code based on your tutorial:

./fastx-length.pl PRJEB511.WBPS9.genomic.fa |gzip >lengths_Nb_WTSI.txt.gz

Can't locate Digest/MD5.pm in @INC (@INC contains: /apps/perl/5.26.1/lib/perl5/x86_64-linux-thread-multi /apps/perl/5.26.1/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./fastx-length.pl line 7.
BEGIN failed--compilation aborted at ./fastx-length.pl line 7.

example.tar.gz
Dear David,
I have been in touch with your scripts to manipulate raw nanopore sequences (twitter, such a nice tool ;) ). Thus, I have used the following command lines just to play with them:

python porejuicer.py raw ugm07_20170510_FNFAE31754_MN19775_mux_scan_Bjar_1005_85455_ch102_read12_strand.fast5 > example/example.raw

signal_viewer.r example/example.raw

Thus, I obtained the attached files and I was wondering how to explain the drop down of raw signal that you can see in the read. I mean, I am planning to perform this on some reads that we suspect that could be some chimeric nanopore reads in order to trim them or to discard for downstream analysis.
Could you help me with this??
Thank you in advance and congratulations for your nice work

I am getting an error when executing the circularAnnotator.r

Error in .geometry(width, height, units, res) : object 'sizeX' not found
Calls: png -> .geometry
Execution halted

Could you explain how to use the stl2svg.pl script?

Thanks in advance!

A nice addition to fast5extractor.py would be to check what data is available in the fast5 (e.g., raw, basecall, etc)