Results for "r"
Bio-Scripts
(base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to D...-> 6e4f1fe62ff1 Step 2/16 : FROM perl:latest ---> de6996f7...--> c0e65f263890 Step 5/16 : RUN apt-get clean && apt-ge...--> e2f4b21b0c27 Step 8/16 : RUN echo "r...1503 days ago
- #Find out a container’s name or ID using the docker ps command: $ docker ps CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 72ca2488b353 my_im...a file from host to container: $ docker cp foo.txt 72ca2488b353:/foo....
1501 days ago
- #This method can be applied directly to FASTA or a FASTQ file, compressed or uncompressed files. Seqtk is a fast and lightweight tool for process...iological data (FASTA/FASTQ). if you have a list of identifiers that you would like to extra...
1463 days ago
Sequence Ids conversion files !
...A/ Name Size Date Modified ARCHIVE/ 02/01/2020, 05:30:00 ASN_BINARY/ 03/07/2020, 07:49:00 GENE...5.1 kB 30/06/2020, 23:01:00 expression/ 06/03/2017, 05:30:00...B 03/07/2020, 14:38:00 special_requests/ 18/04/2020, 00:15:00...nlm.nih.gov/gene/DATA/gene_history.gz ftp://ftp.ncbi.nlm.nih.g...1463 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1461 days ago
get GC across the entire CDS !
#look at GC across the entire CDS. gffread -x - -g | \ seqtk comp - | \ awk -v OFS="\t" '{ print $1, "0", $2, ($4 + $5) / $2 }'1454 days ago
Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001453 days ago
Command to sort the bed file !
#Command to sort the bed file sort -V -k1,1 -k2,2 test.bed1450 days ago
Perl One-Liner to print only non-uppercase letters
#Go through file and only print words that do not have any uppercase letters. perl -ne 'print unless m/[A-Z]/' dna.fa > dnaOnlyLowercase.fa #To lowercase everything perl -pne 'tr/[A-Z]/[a-z]/' dnaUpperCase.fa >dnawithoutuppercase.fa;1444 days ago
Script to extract the cluster detail !
$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic $ cat /proc/cpuinfo | grep -i 'model name' | head -n 1 model name : Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz1439 days ago
