TopHat
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Application data |
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| Created by | Cole Trapnell, Daehwan Kim, Lior Pachter, Steven Salzberg |
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| Biological application domain(s) | RNA-Seq Alignment |
| Principal bioinformatics method(s) | Alignment, mapping |
| Technology | Illumina, SOLiD, 454 |
| Created at | University of Maryland, Center for Bioinformatics and Computational Biology, University of California, Berkeley, Department of Mathematics
Johns Hopkins University, Center for Computational Biology |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | SAM, BED, WIG |
| Programming language(s) | C++ |
| Licence | Boost |
| Operating system(s) | Linux, Unix |
| Contact: | tophat.cufflinks@gmail.com |
Summary: TopHat is a fast splice junction mapper for RNA-Seq reads.
"Error: no local variable "counter" was set." is not a number.
TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner BOWTIE, and then analyzes the mapping results to identify splice junctions between exons.
See also: BOWTIE.
Version 2.0.9 was released in June 2013.
Contents
Using version 1.0.13
Both the following errors disappear under version 1.0.13. i.e. although the HOWTO specifies version 0.7.0, it is written as if you are using version 1.0.13.
Compile error (version 0.7.0)
I found the following error while compiling:
extract_reads.cpp: In function ‘int main(int, char**)’: extract_reads.cpp:178: error: ‘assert’ was not declared in this scope
The solution was to edit the file ../src/extract_reads.cpp:
$diff -c src/extract_reads.cpp~ src/extract_reads.cpp *** src/extract_reads.cpp~ 2008-09-26 03:51:00.000000000 +0100 --- src/extract_reads.cpp 2010-02-17 14:17:40.629202000 +0000 *************** *** 7,12 **** --- 7,13 ---- * */ + #include <assert.h> #include <stdio.h> #include <iostream> #include <set>
A similar problem (and solution) was encountered with the file read_ids.cpp.
Error running tophat (version 0.7.0)
I followed the install guidelines in the HOWTO, but I hit the following problems when running tophat:
$tophat -r 20 test_ref reads_1.fq reads_2.fq tophat: illegal option -- r Error: Maq was not detected on this system. Please verify that Maq is installed and that the Maq executables (maq, fq_all2std.pl) are in your path
Color Space
Latest versions of TopHat support SOLiD color space.
Links
References
To add a reference for TopHat, enter the PubMed ID in the field below and click 'Add'.
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