Results for "Coverage"
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 3287...2210 days ago
- ...rmalization --------------------- -- (Removing Excess Reads Beyond 50 Coverage -- -------------------------...be/Tools/trinityrnaseq-Trinity-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers...
2128 days ago
Install Parrot Virtual Machine !
...long math support..........................yes. auto::perldoc - Is perldoc installed.................................no. auto::coverage - Are coverage analysis tools installed...Ne...1538 days ago
- ...ry: Tools that analyze read coverage to detect copy number variant...-------------------------------------------- Coverage Analysis:...(BETA Tool) Prepares bins for coverage collection SplitInterval...
2076 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2056 days ago
- #!/bin/bash Plot the coverage script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA605.coverage awk '$1 == $chr {print $0}' deduped_MA605.coverage > chr1_MA605.coverage #awk...
2004 days ago
Samtools commands for bioinformatician !
...sults into txt file samtools depth /path/to/sorted_bam.bam > /path/to/coverage_results.txt ### note: return...emoved.bam | awk '{c++;s+=$3}END{print s/c}' ### one liner to count coverage breadth samtools depth -a so...1603 days ago
Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1284 days ago
Tadpole is 250x faster than SPADes assembler !
...igs that did not extend at least this much. mincontig=auto (minc) Do not write contigs shorter than this. mincoverage=1 (mincov) Do not write contigs with average coverage below this. trimends=0...977 days ago
- ...\ out=/dev/null # make 60x haploid coverage for Illumina reads /genetics...oid.fasta.gz \ illuminanames=t addslash=t \ coverage=30 paired=t maxinsert=550 min...cho "best k=${k}" # make 30x haploid coverage for PacBio CLR reads # error...
929 days ago
