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Forum: Bioinformatics 12-03-2013, 02:26 AM
Replies: 0
Views: 591
Posted By LSC
Smile 12-01-2013: Faster and much less memory-required LSC 1.alpha is released

:) 12-01-2013: Faster and much less memory-required LSC 1.alpha is released

In the LSC 0.3.0 or 0.3.1, we optimized the setting of bowtie2 and BWA to get much more short read alignment, which...
Forum: Pacific Biosciences 12-03-2013, 02:24 AM
Replies: 1
Views: 1,866
Posted By LSC
Smile 12-01-2013: Faster and much less memory-required LSC 1.alpha is released

:)12-01-2013: Faster and much less memory-required LSC 1.alpha is released

In the LSC 0.3.0 or 0.3.1, we optimized the setting of bowtie2 and BWA to get much more short read alignment, which...
Forum: Pacific Biosciences 09-30-2013, 11:42 PM
Replies: 0
Views: 1,259
Posted By LSC
Smile 09-30-2013: More robust and faster LSC 0.3.1

09-30-2013: More robust and faster LSC 0.3.1

In LSC 0.3.1, we don't have pseudo chromosome, the alignment time reduced to ~10% (in Bowtie2 mode). And you can re-run some crashed jobs easily now.
...
Forum: Bioinformatics 09-30-2013, 11:40 PM
Replies: 0
Views: 1,007
Posted By LSC
Smile 09-30-2013: More robust and faster LSC 0.3.1

09-30-2013: More robust and faster LSC 0.3.1

In LSC 0.3.1, we don't have pseudo chromosome, the alignment time reduced to ~10% (in Bowtie2 mode). And you can re-run some crashed jobs easily now.
...
Forum: Bioinformatics 08-07-2013, 10:41 PM
Replies: 0
Views: 747
Posted By LSC
Thumbs up 08-07-2013: Big changes in LSC 0.3

08-07-2013: Big changes in LSC 0.3
http://www.stanford.edu/~kinfai/LSC/LSC.html
Many users met problems in downstream analyses by using the LSC output, because some output reads are only...
Forum: Pacific Biosciences 08-07-2013, 10:33 PM
Replies: 1
Views: 2,967
Posted By LSC
Thumbs up 08-07-2013: Big changes in LSC 0.3

08-07-2013: Big changes in LSC 0.3
http://www.stanford.edu/~kinfai/LSC/LSC.html
Many users met problems in downstream analyses by using the LSC output, because some output reads are only...
Forum: Pacific Biosciences 02-06-2013, 05:30 PM
Replies: 8
Views: 2,576
Posted By LSC
Could you please email your run.cfg and...

Could you please email your run.cfg and everything in the temp folder
("ls -ltr") to kinfai@stanford.edu?
Forum: Pacific Biosciences 02-06-2013, 05:29 PM
Replies: 8
Views: 2,576
Posted By LSC
Sorry for the late reply, folks~ I am just sort...

Sorry for the late reply, folks~ I am just sort of busy on another big project currently. I just fixed this bin_path problem in LSC 0.2.3. Please try them and let me know if it works or not.
Forum: Pacific Biosciences 10-17-2012, 04:02 PM
Replies: 0
Views: 987
Posted By LSC
Smile LSC 0.2.2 released and fixes the bug of the option "I_RemoveBothTails".

LSC 0.2.1 ran this option even if you set "N". It may halt the process in LSC 0.2.1 because the read name does not allow "RemoveBothTails". Now you can choose to use this option or not.
Forum: RNA Sequencing 10-13-2012, 08:27 PM
Replies: 0
Views: 678
Posted By LSC
The manual and a tutorial of LSC are released!

Hello SEQanswers Community,

Further Info: http://www.stanford.edu/~kinfai/LSC/LSC.html
http://www.stanford.edu/~kinfai/LSC/LSC_tutorial.html
http://www.stanford.edu/~kinfai/LSC/LSC_manual.html
...
Forum: Pacific Biosciences 10-13-2012, 08:26 PM
Replies: 0
Views: 1,012
Posted By LSC
Smile Default The manual and a tutorial of LSC are released!

Hello SEQanswers Community,

Further Info: http://www.stanford.edu/~kinfai/LSC/LSC.html
http://www.stanford.edu/~kinfai/LSC/LSC_tutorial.html
http://www.stanford.edu/~kinfai/LSC/LSC_manual.html
...
Forum: Bioinformatics 10-13-2012, 08:25 PM
Replies: 0
Views: 585
Posted By LSC
The manual and a tutorial of LSC are released!

Hello SEQanswers Community,

Further Info: http://www.stanford.edu/~kinfai/LSC/LSC.html
http://www.stanford.edu/~kinfai/LSC/LSC_tutorial.html
http://www.stanford.edu/~kinfai/LSC/LSC_manual.html
...
Forum: Pacific Biosciences 10-11-2012, 01:22 AM
Replies: 55
Views: 19,611
Posted By LSC
Sorry of the incompleteness of the website. I am...

Sorry of the incompleteness of the website. I am currently pulled into an emergency project so that I have to postpone the release of the documentation. I hope I could have time to finish the manual...
Forum: Pacific Biosciences 09-14-2012, 03:54 PM
Replies: 55
Views: 19,611
Posted By LSC
In the paper, you will see the accuracy go down...

In the paper, you will see the accuracy go down to <1% when you have enough short reads (SGS) coverage. For those regions without any short reads coverage, the error rate would be still high. Then...
Forum: Pacific Biosciences 09-14-2012, 03:51 PM
Replies: 55
Views: 19,611
Posted By LSC
The paper was accepted last week and is off to...

The paper was accepted last week and is off to print now. The preprint should be on the homepage next week.
Forum: Pacific Biosciences 08-14-2012, 02:59 PM
Replies: 55
Views: 19,611
Posted By LSC
Yes, you just need to copy the scripts to...

Yes, you just need to copy the scripts to overwrite the existing folder
Forum: RNA Sequencing 08-14-2012, 12:46 AM
Replies: 0
Views: 1,153
Posted By LSC
Smile 8-12-2012 - LSC 0.2.1 Released

8-12-2012 - LSC 0.2.1 Released
Please find it at:
http://www.stanford.edu/~kinfai/LSC/LSC.html
The previous thread of LSC is here :
http://seqanswers.com/forums/showthread.php?t=22098

LSC...
Forum: Pacific Biosciences 08-14-2012, 12:45 AM
Replies: 0
Views: 1,469
Posted By LSC
Smile 8-12-2012 - LSC 0.2.1 Released

8-12-2012 - LSC 0.2.1 Released
Please find it at:
http://www.stanford.edu/~kinfai/LSC/LSC.html
The previous thread of LSC is here :
http://seqanswers.com/forums/showthread.php?t=22098

LSC...
Forum: Pacific Biosciences 08-08-2012, 12:00 AM
Replies: 55
Views: 19,611
Posted By LSC
novoalign (V2.07.10) works well in LSC.

novoalign (V2.07.10) works well in LSC.
Forum: Pacific Biosciences 08-07-2012, 03:24 PM
Replies: 55
Views: 19,611
Posted By LSC
Hi Hans Jansen, Your feedback is really...

Hi Hans Jansen,
Your feedback is really helpful. although LSC works well in my computer cluster now, I know there may be something wrong when it is applied in some other systems. Your test is a...
Forum: Pacific Biosciences 08-07-2012, 03:24 PM
Replies: 55
Views: 19,611
Posted By LSC
The paper is in review now (almost the final...

The paper is in review now (almost the final round of the revision). I will post it as this final revision is submitted. Sorry for the inconvenience.
Forum: Pacific Biosciences 07-31-2012, 10:56 AM
Replies: 55
Views: 19,611
Posted By LSC
sorry, the paper is still in review and I just...

sorry, the paper is still in review and I just set up the website. I will fix the problem soon.
Forum: Bioinformatics 07-30-2012, 01:35 PM
Replies: 9
Views: 4,597
Posted By LSC
Smile LSC - a fast PacBio long read error correction tool.

Hello SEQanswers Community,

Further Info: http://www.stanford.edu/~kinfai/LSC/LSC.html

We at the Wong Lab have developed a new tool for error correction of PacBio data. It has been shown to be...
Forum: Pacific Biosciences 07-30-2012, 01:34 PM
Replies: 55
Views: 19,611
Posted By LSC
Smile LSC - a fast PacBio long read error correction tool.

Hello SEQanswers Community,

Further Info: http://www.stanford.edu/~kinfai/LSC/LSC.html

We at the Wong Lab have developed a new tool for error correction of PacBio data. It has been shown to be...
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