Search Results for "bam-readcount"

Pandora FMS is an enterprise-ready monitoring solution that provides unparalleled flexibility for IT to address both immediate and unforeseen operational issues, including infrastructure and IT processes. It uniquely enables business and IT to adapt to changing needs through a flexible and rapid approach to IT and business deployment. Pandora FMS consolidates all the needs of modern monitoring (ITOM, APM, BAM) and provides status and performance metrics from different operating systems, cloud...

miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together...

This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).

ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in "Files"...

MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in...

.../MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles note: 1. Default species is HUMAN. Also supports MOUSE. Can add any other genome if in need. 2. Default format is BED. Also support ELAND. Will add SAM and BAM. 3. –r specifies read length (this is import through my experience). 4. –pe indicates pair-ended data. 5. If data is pair-ended, -isize refers to insert size (total length of a pair).