2016 days ago
Finding Kmers from fasta sequence file
Save it in sample.fa >test TAATGCCATGGGATGTT jellyfish count -m 3 -s 100000 sample.fa -o sample.jf jellyfish dump -c sample.jf It return TGT 1 GAT 1 GGG 1 GGA 1 CAT 1 TGC 1 TAA 1 GCC 1 CCA 1 GTT 1 TGG 1 ATG 3 AAT 11984 days ago
Split the multifasta in separate files !
cat Avaga_allPalindrome.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'1969 days ago
1616 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...1.tar.gz' Content type 'application/x-gzip' length 2152594 byt...1.tar.gz' Content type 'application/x-gzip' length 35536 bytes...flag use... no checking for cat... /bin/cat checking for loc...E=2 -g -c stri_search_class_locate.cpp -o stri_search_class_loc...1562 days ago
To convert just one specific read group to fastq
...info.txt # Select the first N elements. Keep only valid SRR numbers. cat runinfo.txt | cut -f 1 -d , |...n the reads folder. mkdir -p reads # Download the SRR data for each cat selected.txt | parallel fastq...1554 days ago
1519 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 @ 2.10GHz1390 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.chro...1377 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
...xt" | sed 's/^ //g' echo "$text" | sed 's/ \$//g' #Multiple space cat /tmp/test.txt | sed 's/[ ]\+/ /g' echo "$text1" | awk '{ gsub(/[ ]+/," "); print }' cat /tmp/test.txt | awk '{ gsub(/...968 days ago