Results for "read depth"
Bio-Scripts
# get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 #...2207 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in pair...ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining...1_B.fq /path/to/contigs.fasta --threads...2121 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, "2141 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...2137 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...2130 days ago
- ...hase 1: Clustering of RNA-Seq Reads --------------------- ----...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_...
2124 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-d...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|--readi...
2123 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...1534 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...
2120 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Pore...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_...2103 days ago
