b81d45510e
Revision v2
2018-03-16 11:18:06 -04:00
d135feb1a5
response to reviewers' comments, round 2
2018-03-15 21:59:57 -04:00
6e65c5e631
Revision 1
2018-02-09 17:39:02 -05:00
a58b05a61b
extend the section on genome alignment
2018-02-09 13:59:00 -05:00
01560f1db0
Revision v1, to be submitted
2018-02-07 11:07:08 -05:00
39535565ee
first round of revision
2018-02-06 16:19:22 -05:00
680b971bb0
deleted duplicated entries
2018-01-01 19:52:21 -05:00
f159e1c2d3
new section on HPC k-mers
2017-12-24 19:11:23 -05:00
ce8a48d715
fixed two minor typos in references
2017-12-24 13:14:47 -05:00
99879e9e75
a new section on estimating sequence divergence
2017-12-24 12:57:38 -05:00
c969d1a1ce
updated direct RNA-seq results; cite syndip
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and a few minor changes
2017-12-24 11:06:17 -05:00
1617b87ee1
this will become version 3 at arXiv
2017-11-06 10:57:12 -05:00
2191ac58ad
two discussion paragraphs; need one more
2017-11-05 12:27:52 -05:00
c2b09356b8
moved conclusion to result; need new discussion
2017-11-04 22:19:46 -04:00
52ffbc9e0c
added bowtie2 and snap versions
2017-11-02 15:51:23 -04:00
a9790c0f1d
added two bowtie2 numbers for comparison
2017-11-02 15:44:48 -04:00
d0ac78ac08
updated the tech note
2017-11-02 15:37:24 -04:00
1dd221ad82
a bit more on short read mapping
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The tech note still needs improvement. Will do that after the release of v2.3.
2017-10-22 18:38:35 -04:00
beeb806829
r526: fixed a bug when HPC is in use
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It happened when the query HPC minimizer is longer than the reference HPC
minimizer close to the beginning of a contig. We may get a negative coordinate,
which causes an assertion failure.
2017-10-21 19:54:04 -04:00
bd04372873
r524: reverted to bwa-mem end bonus
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and reduced the cost of clipping when filtering by identity
2017-10-20 16:57:31 -04:00
55dcbefe87
updated text (unfinished)
2017-10-20 12:44:54 -04:00
8abba332ad
replaced mapQ plot with sr roc
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figure legend and text to be updated later
2017-10-19 23:43:17 -04:00
bf2d4f7aec
r486: treat "U" as "T" for RNA reads ( #33 )
2017-10-07 18:53:25 -04:00
2833a9c255
150bp mason2 simulation
2017-10-06 09:46:59 -04:00
1c948e0d1d
added GMAP iso-seq numbers
2017-09-20 23:54:02 -04:00
2641613686
various minor improvements
2017-08-25 17:56:16 +08:00
240f6caaff
backup manuscript
2017-08-24 22:05:14 +08:00
b8bdac7e64
backup
2017-08-22 17:45:01 +08:00
19e4b2aab0
backup
2017-08-20 22:10:03 +08:00
8058c85b72
moved appendix to methods; detailed splice aln
2017-08-18 23:33:57 +08:00
53b3265d84
r290: in techrep, explain spliced alignment
2017-08-12 15:40:49 -04:00
0137d0dfab
command lines used for read simulation
2017-08-07 13:41:40 -04:00
648cdd8a3b
minor wording changes
2017-08-04 10:21:10 -04:00
7e231cfd3a
minor wording improvement
2017-08-03 21:28:01 -04:00
95d3c30ae3
rephrasing a bit to avoid the apparent TeX bug
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Several hours sank into this. Damned...
2017-08-03 20:19:00 -04:00
f57fd8c790
added one transition phrase
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as there are no subsubsections now
2017-08-03 18:01:48 -04:00
c70b20ee6d
removed subsubsection
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TeX Live 2016 doesn't work with section and content on the same line.
2017-08-03 17:58:36 -04:00
e8d00a8c8c
removed trailing ^M
2017-08-03 17:20:43 -04:00
ed4efd77bc
minor modifications
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I will submit this version arXiv. There is definitely room for improvement, but
as a semi-formal technical report, it should be good for now.
2017-08-03 12:47:36 -04:00
295874ea30
spell check
2017-08-03 12:17:58 -04:00
9ec5f51afb
the first draft
2017-08-03 12:12:55 -04:00
28ab4d1f72
backup
2017-08-02 22:59:58 -04:00
6c9390b54a
backup
2017-08-02 19:52:31 -04:00
9306299e4d
added benchmark results
2017-08-01 15:12:49 -04:00
d933a263d7
backup
2017-08-01 13:29:02 -04:00
7542b4b40a
Makefile for TeX
2017-08-01 10:42:33 -04:00
d6181de844
added tech notes
2017-08-01 10:38:33 -04:00
8e0d73740e
moved aln-dp.tex to ksw2/tex (a new repo)
2017-06-18 11:21:34 -04:00
7d33acbccc
diagonal global almost working
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one shot, though gaps not left-aligned at the boundary
2017-06-16 12:17:23 -04:00
c4564c31a2
explain DP
2017-06-15 19:37:48 -04:00
Heng Li