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
samtools bedcov bedfile bamfile > output |
Saves the coverage of the sample per position in the bed file |
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blastn
-outfmt |
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 |
-task |
<String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn' > |
-subject |
reference fasta |
-query |
to blast fasta |
-out |
output name |
-perc_identity |
minimum percentage identity |
-word_size |
size of the words used for searching |
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linux commands
df -a |
shows hdd space (also remote) |
sort input.txt | uniq > output.txt |
remove duplicates in file to new file |
Docker
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 |
login |
log into docker hub |
all commands start with docker
GitPitch
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location to presentation |
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