Results for "6"
Bio-Scripts
Install Install Gffcompare on Ubuntu / Linux
...extract, and make a symlink. # download and extract cd ~/workspace/bin wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.9.8.Linux_x86_64.tar.gz tar -xzvf gffcompare...882 days ago
Install StringTie on ubuntu / Linux !
...ink to make it easier to find. # download and extract cd ~/workspace/bin wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.0.Linux_x86_64.tar.gz tar -xzvf stringtie-...882 days ago
Bash script to transfer files to server !
# rsync options source destination rsync -azvh --progress PacBio_clean.fa xxx@xxx.xxx.res.in:/home/ # scp source_file_name username@destination_host:destination_folder scp –rpv /datafile xxx@192.168.1.100:/home/me862 days ago
- ...-- coreutils-8.32 | h7b6447c_0 2.6 MB gawk-5.1.0...-15.6-he881be0_1 perl-archive-tar-2.32-pl526_0 perl-carp-1.38-pl526_3...eflate bioconda::libdeflate-1.2-h516909a_1 --> pkgs/main::libdefla...
844 days ago
- ...graded, 3 newly installed, 0 to remove and 1 not upgraded. Need to get 2,616 kB of archives. After this o...ries currently installed.) Preparing to unpack .../libgslcblas0_2.5+dfsg-6build1_amd64.deb ... Unpackin...
723 days ago
Conda command to install checkV
...--|----------------- boost-1.68.0 |py36h8619c78_1001 325 KB...kcounter-0.1.1 | py36h91eb985_1 871 KB bio...diamond bioconda/linux-64::diamond-0.9.24-ha888412_1...################# | 100% zipp-0.6.0 | 7 KB | ###...694 days ago
Script to rapid genome clustering based on pairwise ANI
...e to perform all-vs-all blastn of sequences: blastn -query -db -outfmt '6 std qlen slen' -max_target_se...ed up the search at the cost of sensitivity: blastn -query -db -outfmt '6 std qlen slen' -max_target_se...694 days ago
- (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000
651 days ago
Identify genome-wide synteny with LASTZ alignment
...low -norna -gff -xmall -lib custom.TE.lib_for_FF.fa FFChr1.txt Step2: Alignment using LASTZ and Chain/Net lastz AAChr1.txt FFChr1.txt K=2200 L=6000 Y=3400 E=30 H=0 O=400 T=1...576 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data477 days ago
