@@ -5,7 +5,7 @@ All tools used in the online tutorial (www.rnaseq.wiki) are referenced below (in
55| ----------| :---------------------|
66| ** Raw data QC** [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/25577376 " >25577376</a >, <a href =" http://www.ncbi.nlm.nih.gov/pubmed/25150838 " >25150838</a >] | FastQC, HTQC [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/23363224 " >23363224</a >] , QC3 [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24703969 " >24703969</a >] , kPAL [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/25514851 " >25514851</a >] . |
77| ** Read trimming** [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24376861 " >24376861</a >] | Trimmomatic [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24695404 " >24695404</a >] , Skewer [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24925680 " >24925680</a >] , Flexbar [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24832523 " >24832523</a >] , FASTX. |
8- | ** Alignment (splice aware, for alignment to a reference genome)** [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24185836 " >24185836</a >] | TopHat [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/19289445 " >19289445</a >, <a href =" http://www.ncbi.nlm.nih.gov/pubmed/23618408 " >23618408</a >] , STAR [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/23104886 " >23104886</a >] , HISAT [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/25751142 " >25751142</a >] , segemehl [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24512684 " >24512684</a >] , GSNAP, MapSplice [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/20802226 " >20802226</a >] , JAGuaR [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/25062255 " >25062255</a >] , SpliceMap [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/20371516 " >20371516</a >] , HMMSplicer [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/21079731 " >21079731</a >] , TrueSight/UnSplicer [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24259430 " >24259430</a >] . |
8+ | **Alignment (splice aware, for alignment to a reference genome)** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24185836">24185836</a>] | TopHat [<a href="http://www.ncbi.nlm.nih.gov/pubmed/19289445">19289445</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23618408">23618408</a>], STAR [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23104886">23104886</a>], HISAT [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25751142">25751142</a>], <a href="http://ccb.jhu.edu/software/hisat2/index.shtml">HISAT2</a>, segemehl [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24512684">24512684</a>], <a href="http://subread.sourceforge.net/">SubRead</a>, GSNAP, MapSplice [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20802226">20802226</a>], JAGuaR [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25062255">25062255</a>], SpliceMap [<a href="http://www.ncbi.nlm.nih.gov/pubmed/20371516">20371516</a>], HMMSplicer [<a href="http://www.ncbi.nlm.nih.gov/pubmed/21079731">21079731</a>], TrueSight/UnSplicer [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24259430">24259430</a>]. |
99| ** Alignment (non splice aware for alignment to a reference transcriptome)** [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/23060614 " >23060614</a >, <a href =" http://www.ncbi.nlm.nih.gov/pubmed/23758764 " >23758764</a >] | BowTie [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/19261174 " >19261174</a >] , Bwa [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/19451168 " >19451168</a >] . |
1010| ** Post-alignment QC** [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/24185836 " >24185836</a >] | FastQC, samtools [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/19505943 " >19505943</a >] , QuaCRS [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/25368506 " >25368506</a >] , RSeQC [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/22743226 " >22743226</a >] , RNA-SeQC [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/22539670 " >22539670</a >] , Picard CollectRnaSeqMetrics, BAMstats, SAMstat [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/21088025 " >21088025</a >] , BlackOPs [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/23935067 " >23935067</a >] , seqbias [ <a href =" http://www.ncbi.nlm.nih.gov/pubmed/22285831 " >22285831</a >] . |
1111| **Gene/transcriptome annotation** [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24722185">24722185</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25319663">25319663</a>] | Annocript [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25701574">25701574</a>], XSAnno [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24884593">24884593</a>], GeneMark-ET [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24990371">24990371</a>], WImpiBLAST [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24979410">24979410</a>], RNASEG [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24780064">24780064</a>], TSSAR [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24674136">24674136</a>], Vicinal [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24623808">24623808</a>], OMIGA [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24609470">24609470</a>], CoRAL [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24145223">24145223</a>], AfterParty [<a href="http://www.ncbi.nlm.nih.gov/pubmed/24093729">24093729</a>], ShortStack [<a href="http://www.ncbi.nlm.nih.gov/pubmed/23610128">23610128</a>], CIRI [<a href="http://www.ncbi.nlm.nih.gov/pubmed/25583365">25583365</a>]. |
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