Results for "discordant read pairs"
Bio-Scripts
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires so...dexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in paire...lin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining...fq /path/to/contigs.fasta --threads N where N is an integer spec...2138 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, "2158 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...2154 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 readi...2147 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(mas....fa.K25.stats.sort --sorted > pairs.K25.stats -opening left.fa.....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 Monday...rinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_108 Mond...
2141 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --hel...ilter by distance between matepairs....Use "unknown" to find matepairs split...ce Filters for individual reads Applied only with --spl...iginal sequence name -I|--readids Append...
2140 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute bytecode for dynamic languages...Is standard C Inf/NaN handling present..............yes. auto::thread - Does your system have threads...1551 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/tra...nce based (if --assembly is given) 2. read mapping based (if --left and...parated --left= Left reads file(s) in FASTQ format, com...onds [ INFO] 2018-07-13 14:54:34 : No reads...
2137 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https:...FASTA/FASTQ of input reads or a directory which will...D_SIZE The number of base pairs at each end of the read...(default: 100) --min_split_read_size MIN_SPLIT_READ_SIZE...se pairs will not be outputted (defaul...2120 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open...while() { chomp; $ids{$_} += 1; } close FILE; local $/ = "\n>"; # read...2110 days ago
