Merge pull request DaehwanKimLab#302 from DaehwanKimLab/3ndoc

add hisat-3n paper link, add hisat2 repo link, update 3n webpage

README.md

@@ -97,6 +97,6 @@ Publication
   Kim, D., Paggi, J.M., Park, C. et al. [Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype](https://www.nature.com/articles/s41587-019-0201-4). Nat Biotechnol 37, 907–915 (2019)
 
 * ### HISAT-3N
-  Zhang, Y., C. Park, C. Bennett, M. Thornton and D. Kim [Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N](https://doi.org/10.1101/gr.275193.120) Genome Research 31(7): 1290-1295 (2021)
+  Zhang, Y., Park, C., Bennett, C., Thornton, M. and Kim, D [Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N](https://doi.org/10.1101/gr.275193.120) Genome Research 31(7): 1290-1295 (2021)
 
 

docs/_layouts/default.html

@@ -113,6 +113,7 @@ <h2>Getting Help</h2>
 			<h2>Publications</h2>
 			<div style="font-size: 0.8em">
 			<ul>
+			<li>Zhang, Y., Park, C., Bennett, C., Thornton, M. and Kim, D. <a class="publication" href="https://doi.org/10.1101/gr.275193.120">Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N.</a> <a class="publication" href="https://genome.cshlp.org"><i>Genome Research</i></a> <b>31</b>, 1290-1295 (2021).</li>
 			<li>Kim, D., Paggi, J.M., Park, C. <i>et al.</i> <a class="publication" href="https://doi.org/10.1038/s41587-019-0201-4">Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.</a> <a class="publication" href="https://www.nature.com/nbt/"><i>Nat Biotechnol</i></a> <b>37</b>, 907–915 (2019).</li>
 			<li>Kim D, Langmead B and Salzberg SL. <a class="publication" href="https://doi.org/10.1038/nmeth.3317">HISAT: a fast spliced aligner with low memory requirements.</a> <a class="publication" href="https://www.nature.com/nmeth/"><i>Nature Methods</i></a> 2015</li>
 			<li>Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. <a class="publication" href="https://doi.org/10.1038/nprot.2016.095">Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.</a> <a class="publication" href="https://www.nature.com/nprot/"><i>Nature Protocols</i></a> 2016</li>

docs/_pages/hisat-3n.md

@@ -115,13 +115,13 @@ For human genome reference, HISAT-3N requires about 9GB for alignment with stand
 
 #### Examples:
 * Single-end slam-seq reads (T to C conversion, RNA) alignment with standard 3N-index:  
-  `hisat-3n --index genome -f -U read.fa -S alignment_result.sam --base-change T,C`
+  `hisat-3n --index genome -f -U read.fa -S alignment_result.sam --base-change T,C --no-repeat-index`
 
 * Paired-end bisulfite-seq reads (C to T conversion, DNA) alignment with repeat 3N-index:   
-  `hisat-3n --index genome -f -1 read_1.fa -2 read_2.fa -S alignment_result.sam --base-change C,T`
+  `hisat-3n --index genome -f -1 read_1.fa -2 read_2.fa -S alignment_result.sam --base-change C,T --repeat --no-spliced-alignment`
 
-* Single-end TAPS reads (have C to T conversion， RNA) alignment with repeat 3N-index and only output unique aligned result:   
-  `hisat-3n --index genome -q -U read.fq -S alignment_result.sam --base-change C,T --unique`
+* Single-end TAPS reads (have C to T conversion， RNA) alignment with repeat 3N-index:   
+  `hisat-3n --index genome -q -U read.fq -S alignment_result.sam --base-change C,T --repeat`
 
 
 
@@ -220,9 +220,9 @@ There are 7 columns in the 3N-conversion-table:
 Publication
 ============
 
-* HISAT-3N paper  
-  Zhang, Y., C. Park, C. Bennett, M. Thornton and D. Kim [Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N](https://doi.org/10.1101/gr.275193.120) Genome Research 31(7): 1290-1295 (2021)
+* HISAT-3N   
+  Zhang, Y., Park, C., Bennett, C., Thornton, M. and Kim, D. [Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N](https://doi.org/10.1101/gr.275193.120). _Genome Research_ **31(7)**: 1290-1295 (2021)
 
 
-* HIAST2 paper  
+* HIAST2   
   Kim, D., Paggi, J.M., Park, C. _et al._ [Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype](https://doi.org/10.1038/s41587-019-0201-4). _Nat Biotechnol_ **37**, 907–915 (2019)  

docs/_pages/links.md

@@ -7,7 +7,8 @@ share: false
 ---
 
 * KimLab - <https://kim-lab.org>
-  * github - <https://github.com/DaehwanKimLab>
+  * lab github - <https://github.com/DaehwanKimLab>
+  * github for HISAT2 - <https://github.com/DaehwanKimLab/hisat2>
 * hisat-genotype - <https://daehwankimlab.github.io/hisat-genotype>
   * github for hisat-genotype - <https://github.com/DaehwanKimLab/hisat-genotype>