2017 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 11985 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 }'1970 days ago
1617 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Download...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...1563 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProjec...the first N elements. Keep only valid SRR numbers. cat runinfo.txt | cut -f 1 -d , |...mkdir -p reads # Download the SRR data for each cat selected.txt | parallel fastq...1555 days ago
1520 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 @ 2.10GHz1391 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...1378 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
text=" ATGGTV AGTGACCTAGAGTGATGA G GGRTTT" echo "$t...echo "$text" | sed 's/ \$//g' #Multiple space cat /tmp/test.txt | sed 's/[ ]\+/...echo "$text1" | awk '{ gsub(/[ ]+/," "); print }' cat /tmp/test.txt | awk '{ gsub(/...969 days ago