srsilva Notas

 Tutorial e Cookbook: https://biopython.org/DIST/docs/tutorial/Tutorial.html Biopython FAQ: https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc5

 mpirun -np 6 /usr/local/bin/mb se o programa não estiver instalado em ambiente conda, não se esqueça de sair dele antes de tentar rodar ;)

 structure_threader run -i Ugibba_filtered1_ref.vcf -o ./results2 -als ~/anaconda3/envs/structure/bin/alstructure_wrapper.R -K 15 -t 3 --ind Ugibba.indfile Fonte: https://radcamp.github.io/Lisbon2020/05_POPULATION_STRUCTURE.html Sendo que o arquivo ind: The “indfile” Open the file with your favorite text editor. If you don’t have one and want to stay on the CLI, you can try the command  nano ~/str_analyses/oyster.indfile  in a new terminal window. The first few lines of this file should look like this: BC1_10_C6 Victoria_BC 4 BC1_20_C6 Victoria_BC 4 BC1_22_C7 Victoria_BC 4 BC1_4_C3 Victoria_BC 4 BC1_7_C5 Victoria_BC 4 BC1_8_C4 Victoria_BC 4 BC1_9_C5 Victoria_BC 4 BC2_10_C5 Klaskino_BC 1

  https://bioinf.shenwei.me/seqkit/ conda install -c bioconda seqkit seqkit rmdup -s < in .fa > out.fa

DOWNLOAD  and collaborate on StructRNAfinder development by accessing in our  GitHub account . All information to install and run it can be accessed there. Installing the stand-alone version:   (Only for linux) To see more details related to the installation process please see the INSTALL file. To install structRNAfinder and its requirements, type in a terminal located in structRNAfinder folder: sudo sh install.sh And follow the provided instructions. Pre-Requisites: StructRNAfinder uses third-part softwares and in-house Perl scripts in order to perform all its workflow. All them are automatically installed and configured when installing the tool. Bellow a list of softwares necessary to use it. Perl Linux perl library libgd-perl ( apt-get install libgd-perl ) Perl package  Bio::Graphics ( cpan install Bio::Graphics ) Infernal RNAfold  from  Vienna package Rfam  covariance models ( Version 12 ) As vezes tem que instalar o Bio::Graphics de novo depois, baixar  RFAM mais novo e dar o coma

 tbl2asn -t ../template_CPs.sbt -i Uf_v2.fasta -j "[organism=Utricularia ] [voucher=xxxx]" -f U_nw. tbl  -V vb