2163 days ago
2149 days ago
2149 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
...F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGcBiasMetrics.jar) R=dat...2149 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/denovo_asm Pro...conda python-consensuscore2: 3.1.0-py27_2...# Please see https://github.com/PacificBiosciences/pbbiocon...2135 days ago
2127 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 12117 days ago
Perl script to split fasta sequence and create overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2117 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 }'2102 days ago
Backward Elimination with Python
#Backward Elimination with p-values...models.formula.api as sm def backwardElimination(x, sl):...1, 2, 3, 4, 5]] X_Modeled = backwardElimination(X_opt, SL)...models.formula.api as sm def backwardElimination(x, SL):...x_rollback = np.hstack((x, temp[:,[0,j]...2100 days ago