Results for "counts"
Blogs
String graph based genome assembly software and tools !
...transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate...2333 days ago
BBTools for bioinformatician !
...sition 19, zero-based). Code: $ kmercountexact.sh in=trimmed.fq out=counts.txt fastadump=f mincount=10 k=20 rcomp=f This will generate a file containing the counts of all 20-mers that occurred...2275 days ago
- +1 more Blogs
Bookmarks
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an hist...1986 days ago
Qualimap2: Evaluating next generation sequencing alignment data
...l User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. Supported types of expe...2067 days ago
- +6 more Bookmarks
Files
- Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3870 days ago
Top-level pages
Next generation sequencing in R or bioconductor environment
...nomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (...tial exon usage); parathyroidSE explains how to generate exon read counts in R DEGseq baySeq (also se...3629 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...https://github.com/warrenlr/LINKS/ Read clustering afcluster Clustering of reads from different genes and different species based on k-mer counts Software (C++) https://gith...2375 days ago
Wire posts
Bio-Scripts
- ...anel of normals for read-count denoising DenoiseReadCounts (BETA Tool) Denoises read counts to produce denoised copy rati...erence NonNFastaSize (Picard) Counts the number of non-N bases in...
2079 days ago
Perl script to create a consensus of nucleotide sequences !
...sort {$b $a} map {length} @mi; # set w to the length of the longest element foreach my $j ( 0 .. $w-1 ){ # Initialize the base counts. my %h = ( a=>0, t=>...2036 days ago
- +3 more Bio-Scripts
Tags
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA bindin...Tags: ChIPulate, Python3, framework, simulate, read, counts, ChIP-seq, experiment
1872 days ago
Comments
- ...p;kallisto h5dump can be used to output an HDF5 file to plaintext. The first line contains a header for each column, including estimated counts, TPM, effective length. run_...
1365 days ago
Comment on "Estimate Genome Size"
...ads2.fastq.gz | jellyfish count -m 31 -o fastq.counts -C -s 10000000000 -U 500 -t 3...# generate a histogram jellyfish histo fastq.counts_0 > fastq.counts_0.histo...inpoint the actual peak find_valleys.pl fastq.counts_0.histo # estimate the size...1902 days ago
- +3 more Comments
