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Search: Posts Made By: Daehwan
Forum: RNA Sequencing 04-10-2012, 05:59 AM
Replies: 3
Views: 3,406
Posted By Daehwan
TopHat 2.0.0 released

TopHat 2.0.0 has been released, which can use Bowtie2 (by the default) as well as Bowtie1. The new version is available at
http://tophat.cbcb.umd.edu/

Detailed information and some instructions...
Forum: Bioinformatics 02-22-2012, 10:10 AM
Replies: 12
Views: 4,666
Posted By Daehwan
Hi guys, This is a memory issue that the...

Hi guys,

This is a memory issue that the tophat_reports program uses too much memory for storing mate pair information that support fusions. A temporary solution is to use a smaller number of...
Forum: Bioinformatics 02-28-2011, 12:39 PM
Replies: 3
Views: 1,322
Posted By Daehwan
I thought I fixed the bug, but it still exists....

I thought I fixed the bug, but it still exists. I'll be grateful if you provide me with your data set so I can fix it? (Daehwan Kim - infphilo@umiacs.umd.edu)

BTW, you can report a bug to...
Forum: Bioinformatics 01-22-2011, 06:57 AM
Replies: 3
Views: 2,145
Posted By Daehwan
I think this is a very good point, I'll make a...

I think this is a very good point, I'll make a new option for users to choose between "n" and "v" option in the next release!!

Thanks,
Daehwan
Forum: Bioinformatics 01-10-2011, 05:18 AM
Replies: 4
Views: 2,339
Posted By Daehwan
Hi guys, I fixed this problem, and we will...

Hi guys,

I fixed this problem, and we will release TopHat 1.2.0 soon!
Forum: Bioinformatics 01-10-2011, 05:15 AM
Replies: 2
Views: 6,352
Posted By Daehwan
Your example is correct, inner distance (in...

Your example is correct, inner distance (in TopHat) = insert length - 2 * read length.
Forum: Bioinformatics 01-02-2011, 03:50 AM
Replies: 6
Views: 2,304
Posted By Daehwan
Hi, We haven't released TopHat 1.2.0, yet.....

Hi,

We haven't released TopHat 1.2.0, yet.. So I guess I gave you some temporary version by email, which didn't include the fix.

For the time being, you might want to change tophat (or...
Forum: Bioinformatics 12-29-2010, 06:27 AM
Replies: 35
Views: 11,113
Posted By Daehwan
Hi agc, I just fixed this "N" bug and the...

Hi agc,

I just fixed this "N" bug and the next version will include the fix.

Daehwan
Forum: Bioinformatics 12-07-2010, 03:58 AM
Replies: 8
Views: 2,790
Posted By Daehwan
@zorph, I need a data set that gives the...

@zorph,

I need a data set that gives the same problem, is it possible for you to open ftp session for your data, I'll just use the data for only test-purpose and delete once I'm done with fixing...
Forum: Bioinformatics 12-06-2010, 06:20 AM
Replies: 8
Views: 2,790
Posted By Daehwan
I'm sorry for the problem, would any of you mind...

I'm sorry for the problem, would any of you mind providing me with data set that cause the problem? (infphilo at cs.umd.edu) or you can reduce the number of reads while having the problem and give me...
Forum: Bioinformatics 12-03-2010, 08:33 AM
Replies: 14
Views: 3,517
Posted By Daehwan
-p is the number of threads you want to run on...

-p is the number of threads you want to run on each node. I think you just need to run n lanes on n nodes. However, if your node has a multicore processor, you can specify -p "# of cores" in each...
Forum: Bioinformatics 12-02-2010, 03:46 AM
Replies: 3
Views: 1,863
Posted By Daehwan
This is a bug due to variable read length, which...

This is a bug due to variable read length, which we fixed, the next version will include the fix.
Forum: Bioinformatics 11-29-2010, 03:39 AM
Replies: 4
Views: 6,455
Posted By Daehwan
This is a bug in TopHat, we fixed this and will...

This is a bug in TopHat, we fixed this and will post a new version soon.

Thanks,
Daehwan
Forum: Bioinformatics 11-27-2010, 03:22 AM
Replies: 6
Views: 2,304
Posted By Daehwan
I'll fix this problem in the next release of...

I'll fix this problem in the next release of TopHat.
Forum: Bioinformatics 11-16-2010, 08:48 AM
Replies: 1
Views: 2,675
Posted By Daehwan
I just sent you an email. One thing you can try...

I just sent you an email. One thing you can try is to use "--keep-tmp" option not to delete the temporary files including tmp/accepted_hit.sam, and taking a look at them will probably give you some...
Forum: Bioinformatics 11-05-2010, 07:11 AM
Replies: 2
Views: 2,048
Posted By Daehwan
The current version (1.1.2) checks the distance...

The current version (1.1.2) checks the distance between the paired reads. If the distance is longer than #mate-inner-dist + mate-std-dist#, it doesn't output such a pair. So, I think it's probably a...
Forum: Bioinformatics 11-02-2010, 07:24 AM
Replies: 9
Views: 4,049
Posted By Daehwan
I see, samtools is actually different from...

I see, samtools is actually different from samtools.pl - samtools is located under your_samtools_directory instead of your_samtools_directory/misc
Forum: Bioinformatics 11-02-2010, 07:19 AM
Replies: 4
Views: 3,711
Posted By Daehwan
TopHat maps left and right reads separately using...

TopHat maps left and right reads separately using Bowtie, that is, it doesn't use Bowtie's pair searching like --fr, --rf, --ff. Using the mapped reads, TopHat finds pairs if the two reads of a pair...
Forum: Bioinformatics 11-02-2010, 07:06 AM
Replies: 9
Views: 4,049
Posted By Daehwan
TopHat runs "samtools" instead of "samtools.pl" -...

TopHat runs "samtools" instead of "samtools.pl" - it's probably because you didn't install samtools like "make install" (although I never installed samtools myself before).
Forum: Bioinformatics 11-02-2010, 07:02 AM
Replies: 1
Views: 1,862
Posted By Daehwan
As you know, TopHat is a spliced read mapper, and...

As you know, TopHat is a spliced read mapper, and for unmapped reads, TopHat tries to fill the gaps in them using user-provided or novel junctions (closures), but for some gaps, there seem to be more...
Forum: Bioinformatics 11-02-2010, 06:54 AM
Replies: 9
Views: 4,049
Posted By Daehwan
TopHat expects samtools just like bowtie. (sorry...

TopHat expects samtools just like bowtie. (sorry for the incorrect error message)

And TopHat runs samtools, which gives the following message on my server:
...
Forum: Bioinformatics 10-29-2010, 05:45 AM
Replies: 6
Views: 1,960
Posted By Daehwan
Did you run "make install"? If yes, you can run...

Did you run "make install"? If yes, you can run tophat using your_tophat_directory/bin/tophat.

Otherwise, there should be some problem regarding TopHat installation.
Forum: Bioinformatics 10-29-2010, 05:36 AM
Replies: 4
Views: 1,729
Posted By Daehwan
Please note it is also explained in README.

Please note it is also explained in README.
Forum: Bioinformatics 10-27-2010, 09:39 AM
Replies: 2
Views: 1,877
Posted By Daehwan
I think it's probably due to quality values, you...

I think it's probably due to quality values, you know, the quality value of each base usually decreases from left to right. So, if we reverse-complement a read, the read will have low quality values...
Forum: Bioinformatics 10-05-2010, 09:48 AM
Replies: 22
Views: 6,768
Posted By Daehwan
Since you are using -C, which is for colorspace...

Since you are using -C, which is for colorspace read, you need to use colorspace reads instead of nucleotide reads.
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