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overview Cheat Sheet (DRAFT) by


This is a draft cheat sheet. It is a work in progress and is not finished yet.

GIT commands

git remote add origin ssh://gt
adds the remote git to the local git repository
git push origin master
pushes the local git to the remote repository


samtools bedcov bedfile bamfile > output
Saves the coverage of the sample per position in the bed file


0 = pairwise, 1 = query-­anc­hored showing identi­ties, 2 = query-­anc­hored no identi­ties, 3 = flat query-­anc­hored, show identi­ties, 4 = flat query-­anc­hored, no identi­ties, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1, 10 = Comma-­sep­arated values, 11 = BLAST archive format (ASN.1), 12 = JSON Seqalign output, 13 = JSON Blast output, 14 = XML2 Blast output
<St­ring, Permis­sible values: 'blastn' 'blast­n-s­hort' 'dc-me­gab­last' 'megab­last' 'rmblastn' >
reference fasta
to blast fasta
output name
minimum percentage identity
size of the words used for searching
blastn -help

linux commands

df -a
shows hdd space (also remote)
sort input.txt | uniq > output.txt
remove duplicates in file to new file


run <im­age>
creates a container from image, and starts it
start <na­me|­id>
starts a stopped container by name/id
stop <na­me|­id>
stops a running container by name/id
ps [-a]
shows all contai­ner­s/i­ncludes stopped containers
rm <na­me|­id>
removes container from the machine
log into docker hub
all commands start with docker