• 5' : left
• 3' : right

;-)

Not completely bioinformatics oriented, but some things I've found handy.

#subtract a small file from a bigger file
grep -vf filesmall filebig

#use awk to rearrange columns
awk '{print $2 " " $1}' file.txt

#sort a bed file by chrom, position
sort -k1,1 -k2,2n file.bed > file.sort.bed

#strip header
tail +2 file > file.nh

#find and replace over multiple files
perl -pi -w -e 's/255,165,0/255,69,0/g' *.wig

#print line 83 from a file
sed -n '83p'

#insert a header line
sed -i -e '1itrack name=test type=bedGraph' file.bed

#sum column one from a file
awk '{s+=$1} END {print s}' mydatafile

I have a vision of this cheat sheet being an extensive, very convenient set of environment variables and man pages. It should be versioned and should be on something like GitHub.

For example:

####################
# HG19
####################
$CHR1_SIZE=249250621
$CHR2_SIZE=243199373
...

####################
# Shortcuts
####################
$SUMCOL='awk '\''{ SUM += $1} END { print SUM}'\'

Other informational stats should be rolled into "man" entries. For example,

man dna
man iupac
man 2_powers
man log_examples

This may be utterly harebrained, but it seems useful to me. A community-based, focused wikipedia and shortcut library on the command line.

missing from the list

• 1 nucleosome = 147bp
• Crude AA to kilo dalton conversion = AA No X 0.11 =Kd
• Perl one liners for text conversion
• s/015012/012/ # Windows -> Unix
• s/012/015012/ # Unix -> Windows

I have a collection of handpicked reference cards. It helps every now and then.

I prefer to call it as a Bioinformatician's Pocket Reference!!

Correspondance between the genome version nomenclature : hg19 (UCSC) = GRCh37 (NCBI)

This reminds me a little bit of BioNumbers: http://bionumbers.hms.harvard.edu

• AUG = Initiation

• UAA, UGA, UAG= Termination

• AT= 2 Hydrogen Bond, GC =3 Hygrogen Bond and adjacent bases are separated by 3.4Å

• Purine= Adenine & Guanine AND Pyrimidines= Cytosine, Uracil & Thymine

• DNA replication is semi-conservative

Coming more.... :D

• Amino acid weights, IEPs
• some FASTA statistics one-liners
• quick overview of possible cli BLAST inputs/outputs (reading -help takes so long as they are all over the place)
• BLAST tabular output column names
• Karlin-Altschul formula
• definition of PAM and BLOSUM
• order of AAs in a substitution matrix/PSSM

The cheat sheet for programming in R would be what you are looking for.

Here are good manuals that my advisor, Thomas Girke, wrote:

• R & Bioconductor Manual
• HT Sequence Analysis with R and Bioconductor

The HT Sequence Analysis manual was as recommended in Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources

I'll start off with a few of my own:

• an alpha-helix has 3.6 residues per turn

• A haploid human genome has a little over 3 billion bases and contains around 20,000 genes

• A handy alias for summing up a column of numbers from the command line:

  sumcol='awk '\''{ SUM += $1} END { print SUM}'\'

I would like a cheat sheet of arguments for common bioinformatics executables (e.g. blast, clustal, bowtie, bwa, fastx-toolkit), the popular bioperl scripts (like bp_seqfeature_load.pl), as well as the most common bioinformatics things in bash (e.g. mass renaming: foreach f in *fasta; do mv $f `echo $f | sed -e 's/.fasta/.fa'` done)

My cheat sheet would contain the length of the human chromosomes.

building up my list here.. a blog post would be a good record for myself when i change computers or move office where i usually lose my printed copies.

http://kevin-gattaca.blogspot.com/2011/03/cheat-sheets-galore-bioinformatics.html

Very cool question, here's mine, which probably isn't all that relevant to most biostar members but is popular in our lab:

A table of nucleotide substitution models, and how to set them in the most commonly used programs

Still working on it (you can implement the exotic models in most of the software, but not easily)

My cheat sheet would be

Amino acid structures with their properties

And I would also consider Biostar because it is in fact more than google.

A useful addition would be a landscape or flowchart how to get from one file (format) into the next..... bioinformatics is about parsing it right....... :)

I like this question, so at the risk of sounding trite: my cheat sheet = a Google search. I store very little information these days; it's as quick and easy to search for it as and when required.

Great ideas! I'd add a Blosum62 substitution matrix to the list.

List of most used file formats (.pdb, .bam, .fastq, etc etc), what information they contain, and what they can be used for? (and possibly the most well-known software(s) that reads them)

great idea!

a bit of biology:

the citrus cycle! http://student.ccbcmd.edu/~gkaiser/biotutorials/cellresp/images/u4fg35.jpg

or here you can find it also along other must-knows

for R & Regex I already have separate cheatsheets on my desk. One thing I am missing tough, is a cheatsheet for Regex, referring to in which environment one has to escape which characters and back-references (\ or $)

Biology by the numbers

http://www.rpgroup.caltech.edu/publications/SnapShot2010.pdf

• No. seqs(fasta):

  grep \> file_name | wc -l
  

##Tabulated BLAST header
qseqid sseqid pident alignlength mismatch gapopen qstart qend sstart send evalue bitscore **- **

## go to the end of file in Vi editor
G (shift + g )** **

##substitute in Vi editor

:%s/Soxgene/Foxgene/g

##remove exact duplicate sequences from fasta file

sed -e '/^>/s/$/@/' -e 's/^>/#/' file.fasta | tr -d '\n'|tr "#" "\n"| tr "@" "\t" |sort -u -t ' ' -f -k 2,2 |sed '/^$/d'|sed -e 's/^/>/' -e 's/\t/\n/'

##remove blank lines
sed '/^$/d' file.fasta >Noblanks_file.fasta.out