Results for "SAM tool"
Top-level pages
List of visualization tools for genome alignments
...of genome alignment visualization tools, which could be useful for...iew Genome browser and annotation tool that allows visualization of...tm JVM Java Visual Mapping tool for NGS reads http://www.spr...vigo.es/pileline/pilelinegui.html SAMtools tview Simple and f...2277 days ago
Webinar on RNA-Seq Data Analysis on 28 Feb 2018
Strand NGS is a biologist friendly NGS analysis tool that allows biologists to an...ght the use of Strand NGS features such as PCA, sample correlation, clustering, Ve...orts large scale RNA-Seq data analysis too. The tool also supports biological cont...2257 days ago
Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes
Horizontal gene transfer (HGT), the “non-sexual movement of genetic material...in the recipient genome and provide novel function. Following are the popular tool to detect HGT in genomes: T-...843 days ago
Some useful Bioinformatics links
...abyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/ Tool documentation https://broad...nswers http://seqanswers.com/forums/showthread.php?t=26721 samtools(1) manual page http://www.htslib.org/doc/samtools.html How To Filter Mapped...2234 days ago
- ...split bam files into sets with mapped and unmapped reads: samtools view -F4 sample.bam > sample.mapped.samsamtools view -f4 sample.bam > sam...rst=$5;}; last=$5;} END {print last-first}' myfile.txt To sample only 200 first bases from a...
2210 days ago
Tools to Predict the Impact of Missense Variants !
...f new variants. Study of 10 tools on five datasets that such a...ty: they arise due to (1) the same variants or (2) different variants from the same protein occurring both in the...letion (CADD)“CADD is a tool for scoring the deleteriousne...2196 days ago
Protein-Protein Interaction Sites Predictions !
The study of Protein–Protein Interactions (PPIs) h...nical observations. Following are the list of tools commonly used to PPIs predic...ins for proteins with known 3D structure. PFplus A tool for extracting and displaying...2195 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumi...with GapFiller". There are also some tools like GAPresolution that can...//www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformati...particular, take a look at the IMAGE tool: http://genomebiology.com/201...2158 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r...gt; r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r...bwa/hs37m.fa r12.fq > r12.bwasw.sam gsnap -A sam -d hs37m r1...py -g hs37m -h hs37m -o r12.stampy.sam...2175 days ago
- The benchmark module is a great tool to know the time the code takes to run. The output is usually in terms of CPU time. This module provides us with a way to optimize our code. With...
2073 days ago
