2030 days ago
2016 days ago
2016 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:"...); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sor...aln-pe.mapped.sorted.${i}_GCBias.txt CHART=aln-pe.mapped.sorted.${i}_GC...2015 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/an...-py27_0 conda-forge mkl_random:...for, we make no warranty regarding any # # Bioconda...2002 days ago
1993 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 11984 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, "1984 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 }'1969 days ago
Backward Elimination with Python
#Backward Elimination with p-values only: import statsmodels.formula.api as sm def backwardElimination(x, sl): numVars = len(x[0]) for i in ra...stype(float) if maxVar > sl: for j in r...lues[j].astype(float) == maxVar): temp[:...1967 days ago