Results for "split reads"
Bio-Scripts
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( -form...2138 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for read...d $id && defined $seq){ $map{$id} = $seq; $seq=""; } ($id) = split(' '...2132 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git...building a k-mer catalog from reads) -- ------------------------..._normalization/tmp_normalized_reads Normalization complete....6.6/trinity_out_dir/chrysalis/readsToComponents.out > /home/urbe/...6/trinity_out_dir/partitioned_reads.files.list.ok Monday, July 9...
2126 days ago
- ...split into individual reads --split-spot...e "unknown" to find matepairs split...ce Filters for individual reads Applied only with --spl...reads and above are ignored. -G...
2125 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2124 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This i...$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.out.sa...pping with $toolName" if [ $readsType == "ont" ]; then $n...2122 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/tr...arated --left= Left reads file(s) in FASTQ format, comm...rated --right= Right reads file(s) in FASTQ format,...nds [ INFO] 2018-07-13 14:54:34 : No reads provided, skipping read diagn...
2122 days ago
Installing Porechop on Ubuntu !
...hreshold END_THRESHOLD] [--no_split] [--discard_...SIDE] [--min_split_read_size MIN_SPLIT_READ_SIZE...adapters found at the ends of reads (default: 2) --end_thresho...eads with middle adapters are split) (...2105 days ago
- ...for coverage collection SplitIntervals Split intervals into sub-interval f...Step 2: Aligns reads to the microbe reference...rd) Splits SNPs and INDELs into separat...
2074 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fas...chomp; next unless /\w/; s/>$//gs; my @chunk = split...2065 days ago
