What is TopHat in RNA-Seq?
TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites.
What are bowtie TopHat and cufflinks?
TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data.
How do I install TopHat2?
Building TopHat
- Unpack the TopHat source tarball: tar zxvf tophat-2.0.0.tar.gz.
- Change to the TopHat directory: cd tophat-2.0.0.
- Configure TopHat using the ./configure script.
- Finally, make and install TopHat.
What is HISAT2?
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Based on an extension of BWT for graphs [Sirén et al.
What is tophat used for?
Top Hat is currently used by 750 of the top 1,000 postsecondary institutions to deliver interactive readings and assignments, host polls and discussions, manage assessments and gain rich insights into student progress and performance to enhance the learning experience.
What is FPKM value?
FPKM stands for fragments per kilobase of exon per million mapped fragments. It is analogous to RPKM and is used specifically in paired-end RNA-seq experiments [17].
What is StringTie?
Overview. StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
What is bowtie2?
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s of characters to relatively long (e.g. mammalian) genomes.
How do I run bowtie2 on Ubuntu?
Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU make (usually with the command make, but sometimes with gmake) with no arguments. If building with MinGW, run make from the MSYS environment. This should install bowtie and you should be able to run /pathtofolder/bowtie-0.12.
Is HISAT2 splice aware?
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts 2) is also a splice-aware aligner using a graph-based alignment approach (graph Ferragina Manzini index) that can align DNA and RNA sequences [13].
Can top hat detect cheating?
Create digital tests with Top Hat Test
Top Hat Test tackles the issue of cheating head-on by allowing professors to create digital tests that students can take on their own devices—no need to collect students’ smartphones, tablets or laptops before an exam.
Is top hat an LMS?
A learning management system (LMS) provides professors and students with valuable academic infrastructure, housing course rosters and grades. However, an active learning platform, such as Top Hat, is a necessity in order to elevate the learning experience for your students.
What does a high FPKM mean?
FPKM is used especially for normalizing counts for paired-end RNA-seq data in which two (left and right) reads are sequenced from the same DNA fragment. Generally, the higher the FPKM of a gene, the higher the expression of that gene.
What is the difference between TPM and FPKM?
The only difference between RPKM and FPKM is that FPKM takes into account that two reads can map to one fragment (and so it doesn’t count this fragment twice). TPM is very similar to RPKM and FPKM. The only difference is the order of operations.
How does StringTie merge work?
In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples.
What is bowtie2 alignment?
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
What is the difference between bowtie and bowtie2?
The chief differences between Bowtie 1 and Bowtie 2 are: For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.
What is quasi mapping?
Quasi-mapping and quantification
The quasi-mapping approach estimates where the reads best map to on the transcriptome through identifying where informative sequences within the read map to instead of performing base-by-base alignment.
What is a splice aware aligner?
A splice-aware aligner would know not to try to align RNA-seq reads to introns, and would somehow identify possible downstream exons and try to align to those instead, ignoring introns altogether.
Are Top Hat quizzes monitored?
Since the test is non-monitored, students will be able to leave the test environment to access any additional web pages, tools or programs they may need. If a timer has been applied, it will continue to count down if a student navigates away from the test (or exits Top Hat entirely).
Are Top Hat exams proctored?
Completing a Remotely Monitored Test
After paying for each required item, students will be able to proceed into the course. *Purchasing the “Remote Proctored Exams (1 Course Access)” item when enrolling in a Top Hat course grants students the ability to take remotely proctored tests in that course only.
What is a Top Hat tool used for?
What Is It? Top Hat is a platform for building and conducting interactive slideshow presentations. Through a built-in student-response system, students can use their own mobile devices to take part in ongoing, live assessments during a lecture.
Is Top Hat SaaS?
As Top Hat’s Chief Revenue Officer, Matt Schurk leads all revenue-generating functions, including sales and customer support. Schurk is a seasoned SaaS go-to-market leader with a proven track record of building high-performing and mission-driven teams.
How do you interpret FPKM values?
The interpretation of FPKM is that if you sequence your RNA sample again, you expect to see for gene i, FPKMi reads divided by gene i length over a thousand and divided by the total number of reads mapped over a million.
What does RPKM correct for?
RPKM stands for Reads Per Kilobase of transcript per Million mapped reads. FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads. In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it.