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=Programs about mRNA-seq= | =Programs about mRNA-seq= | ||
| − | I only | + | I only listed programs I use regularly, for a more complete list, please check [[http://seqanswers.com/wiki/SEQanswers|SeqWiki]]. |
==QC== | ==QC== | ||
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*[https://trac.nbic.nl/passion/ PASSion] | *[https://trac.nbic.nl/passion/ PASSion] | ||
*[http://research-pub.gene.com/gmap/ GSNAP] | *[http://research-pub.gene.com/gmap/ GSNAP] | ||
| + | *[https://github.com/alexdobin/STAR STAR] | ||
==Processing== | ==Processing== | ||
| − | *[ | + | *[http://samtools.sourceforge.net/ SAMtools] |
| − | *[bedtools] | + | *[http://code.google.com/p/bedtools/ BEDtools] |
| − | *[HTseq-count] | + | *[http://www-huber.embl.de/users/anders/HTSeq/doc/count.html HTseq-count] |
==Quantification== | ==Quantification== | ||
| − | *[Cufflinks] | + | *[http://deweylab.biostat.wisc.edu/rsem/ RSEM] |
| − | *[Scripture] | + | *[http://cufflinks.cbcb.umd.edu/ Cufflinks] |
| − | *[SpliceTrap] | + | *[http://www.broadinstitute.org/software/scripture/ Scripture] |
| + | *[http://rulai.cshl.edu/splicetrap/ SpliceTrap] | ||
| + | |||
| + | ==Differential expression== | ||
| + | |||
| + | *[http://www.bioconductor.org/packages/release/bioc/html/edgeR.html edgeR] | ||
| + | *[http://cufflinks.cbcb.umd.edu/manual.html Cuffdiff] | ||
| + | *[http://www-huber.embl.de/users/anders/DESeq/ DESeq] | ||
| + | *[http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html DEXseq] | ||
| + | |||
| + | =Useful websites about splicing= | ||
| + | |||
| + | *[http://www.life.umd.edu/labs/mount/RNAinfo/ RNAinfo, A website about RNA] | ||
| + | *[http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home ESEfinder] | ||
| + | *[http://sfmap.technion.ac.il/ SFmap] | ||
| + | |||
| + | =Communities= | ||
| + | |||
| + | *[http://seqanswers.com/ SEQanswers] | ||
| + | *[http://www.rna-seqblog.com/ RNAseq blog] | ||
| + | *[http://www.biostars.org/ Biostar] | ||
Latest revision as of 20:52, 15 June 2016
Contents |
[edit] Programs about mRNA-seq
I only listed programs I use regularly, for a more complete list, please check [[1]].