CATEGORY Next Gen Seq
Women in Science Program
Today 4pm, Prof. Caroline Friedel (LMU) will give a talk on „Deciphering the interplay between virus-induced read-through transcription, RNA decay and loss of transcription in HSV-1 lytic infection“ in the newly established Women-in-Science-Program of the Faculty of Mathematics and Computer Science of the University of Marburg. Room 04A30, Hans-Meerwein-Straße 6, 35032 Marburg.
SSPACE – Can’t locate getopts.pl
Today I tried to run the SSPACE Standard perl script for doing scaffolding of pre-assembled contigs, but I got this error message: Can’t locate getopts.pl in @INC (@INC contains: /Tools/SSPACE-STANDARD-3.0_linux-x86_64/dotlib/ /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at SSPACE_Standard_v3.0.pl line 124. getopts.pl is a Perl 4 core library but no longer included in…
How to run velvet with OPENMP
Just few steps to make velvet working for de novo genome assembly using multiple CPU cores: 1) Download the latest version of velvet from http://www.ebi.ac.uk/~zerbino/velvet/ 2) $ tar -xzvf velvet_1.2.10.tgz 3) $ cd velvet_1.2.10 4) Edit the Makefile to compile with a higher Kmer length and enable longsequences for contigs longer than 32kb: $ vim…