Results for "read"
Bio-Scripts
Mapping with BWA-mem or BWA-sampe in one go with python script !
...d and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in...com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining.../lib1_B.fq /path/to/contigs.fasta --threads N where N is an integer spe...2116 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2136 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 her...2132 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 reading $file:$!\n"); while(){...2125 days ago
- ...building a k-mer catalog from reads) -- -----------------------....6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_2_...rinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_2 Monda...rinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_108 Mon...
2119 days ago
- ...split into individual reads --split-spot...et, otherwise - to individual reads -M|--minReadLen...ce Filters for individual reads Applied only with --sp...iginal sequence name -I|--readids Append...
2118 days ago
Install Parrot Virtual Machine !
...has timespec.......................yes. auto::infnan - Is standard C Inf/NaN handling present..............yes. auto::thread - Does your system have threads.......................yes....1529 days ago
- ...1. sequence based (if --assembly is given) 2. read mapping based (if --left and...comma-separated --left= Left reads file(s) in FASTQ format, com...in 13 seconds [ INFO] 2018-07-13 14:54:34 : No reads provided, skipping read diag...
2115 days ago
Installing Porechop on Ubuntu !
...g build/lib/porechop/nanopore_read.py -> /home/urbe/anaconda3/li...te-packages/porechop/nanopore_read.py to nanopore_read.cpython-3...FASTA/FASTQ of input reads or a directory which will...(default: 100) --min_split_read_size MIN_SPLIT_READ_SIZE...2098 days ago
Perl script to extract sequence by Ids from multifasta file !
...; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1; } close FILE; local $/ = "\n>"; # read by FASTA record open FASTA...2088 days ago
