Results for "6"
Bio-Scripts
...s, and set $PATH to use this Perl instead of the system Perl: export PERL5LIB="$PERL_BASE/perl-5.24.1/lib/perl5:$PERL_BASE/perl-5.24.1/lib/perl5/x86_64-linux:$PERL5LIB" export PAT...2193 days ago
Perl script to count number of Ns in a multifasta file !
...d1_size15575755 15575755 71824 0.00463263155647429 scaffold2_size1063...0597248282801474 scaffold11_size2396892 2396892 6066 0.00253719844...0.0390421929048817 scaffold30_size864014 864014 80076 0.1021458329...ize51859 51859 0 0 scaffold79_size46742 46742 0 0 scaffold80_size...2193 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name h...2189 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -fo...2187 days ago
- ...e/urbe/Tools/augustus-3.2.3/config #run BUSCO python BUSCO.py -i /media/urbe/MyDDrive/longMIRA_canuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30...
2186 days ago
Long reads mapper bash script !
...#Location of the tools samtools=/home/urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools/graphmap/bin/Linux-x64/graphmap minimap2Loc=/home/urbe/Tools/minimap2-2.3_x64-linux/minimap2 bwaMemLoc=/h...2171 days ago
- ...ools/trinityrnaseq-Trinity-v2.6.6/util/..//util/support_scrip...ools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa bo...ools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partit...ools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/read_partit...
2176 days ago
- ...ssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate _...ssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate --assembly=Trini...-13 14:54:34 : largest 22136 [ INFO] 2018-07-13 14:54:34...
2172 days ago
- ...sf.io/xju4a/download", "ERR458501": "https://osf.io/nmqe6/download",...mple_links.keys() # download yeast rna-seq data from Schurch et al, 2016 study rule download_all:...
1565 days ago
Installing Porechop on Ubuntu !
...100% (1579/1579), 3.38 MiB | 1.62 MiB/s, done. Resolving deltas: 100% (869/869), done. Checking connec...ome/urbe/anaconda3/lib/python3.6/site-packages/porechop copyi...ome/urbe/anaconda3/lib/python3.6/site-packages/porechop copyi...(default: 16) Barcode binning settings:...2154 days ago
