1399 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 @ 2.10GHz1375 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip -...1362 days ago
1337 days ago
1200 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...s::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all th..., $file); #print $code; my $ae = Archive::Extract->new( archive => $file); m...ilva_LSU_code; my $silva_LSU_ae = Archive::Extract->new( archive => $silva_LSU_f...1157 days ago
1155 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt993 days ago
Extract the values using ids !
#Awk script awk 'NR==FNR{tgts[$1]; next} $1 in tgts' file1 file2 Look: $ cat file1 11002 10995 48981 79600 $ cat file2 10993 item 0 11002 item...891 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas886 days ago