BOL

Ten steps to get started in #Genome #Assembly and #Annotation https://f1000research.com/articles/7-148/v1

Bioinformatics resources https://github.com/danielecook/Awesome-Bioinformatics #Bioinformatics #Resources

Assessing an effective undergraduate module #teaching applied #bioinformatics to biology students http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005872

Bioinformatics tools collection and database https://bio.tools #tools #database #search #list

Marginal plot in R https://stackoverflow.com/questions/8545035/scatterplot-with-marginal-histograms-in-ggplot2 #R #Plot #Marginal

Random forest algorithms http://blog.yhat.com/posts/random-forests-in-python.html #forest #random #algo

Toy example comparing several MSA algorithms http://wiki.bits.vib.be/index.php/Multiple_sequence_alignment #Alignment #MSA #Algorithms

Remove "|" from fasta header. $ sed 's,|,_,g' -i file.fa #fasta #header #sed

Remove unwanted character from fasta file. sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa #fasta #file #header #charater

Evolution and phylogeny software http://tree.bio.ed.ac.uk/software/ #tools #software #phylogeny #evolution

You can use the df command to know the free space in the disk: $ df -h . #df #Linux #List #Free #Space

To know the size of the directory in current folder. $ du -sh * #Size #Directory #List #Space #Linux #du

Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}' #Fasta #Count #Bases

Convert masked genome to N letters. $ perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna #Genome #Masked #N #Convert

Unmasking the lower case values in genome. $ perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #Genome #Unmask #Perl #Oneliner