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Search: Posts Made By: ldong
Forum: Bioinformatics 08-20-2013, 06:28 AM
Replies: 13
Views: 6,514
Posted By ldong
Hi, AL_B, My understand is that the script,...

Hi, AL_B,
My understand is that the script, compile.py reads all the and .fa files, and extract many short sequences with length of 'merlen", then map the short sequences back to the fa files, so...
Forum: Bioinformatics 12-07-2010, 04:42 PM
Replies: 31
Views: 8,857
Posted By ldong
Hi, Dinesh, Thanks for your feedback. If...

Hi, Dinesh,
Thanks for your feedback.
If the big file size is the issue, we can try to create smaller Excel file. Anyway, we just want to get a small number of candidates to give a closer look....
Forum: Bioinformatics 12-04-2010, 03:59 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi, Jun, Sorry I didn't see your post earlier....

Hi, Jun,
Sorry I didn't see your post earlier. I treat c and j as novel transcripts. His is my script to find them. Feedbacks are welcome:

#!/usr/bin/perl

use Spreadsheet::WriteExcel;
use...
Forum: Bioinformatics 11-02-2010, 08:33 AM
Replies: 13
Views: 6,514
Posted By ldong
Ok. The sgr files created by creat_signial.pl...

Ok. The sgr files created by creat_signial.pl will be used by score_hits.pl to look for potential peaks. The original creat_signal.pl read eland output, you need modify it to read bowtie output. It...
Forum: Bioinformatics 11-02-2010, 07:50 AM
Replies: 13
Views: 6,514
Posted By ldong
Hi, dnusol, merlen is the length of your...

Hi, dnusol,
merlen is the length of your reads. compile.py uses the number to get a piece of sequence of that length and map back to genome to see if there are same sequence elsewhere. So if your...
Forum: Bioinformatics 10-28-2010, 05:02 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi, Jun, Here is the script. Any feedback is...

Hi, Jun, Here is the script. Any feedback is welcome. Best, ldong

#!/gpfs/runtime/bin/perl

use Spreadsheet::WriteExcel;
use strict;

my %gene;
my %alter;
Forum: Bioinformatics 10-09-2010, 07:26 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi, tguo, I think the reason is that reference...

Hi, tguo,
I think the reason is that reference sequence ID in mm9 does not match the chromosome Id in the GTF file.
By the way, where did you download the UCSC GTF file? Could you remind me? I...
Forum: Bioinformatics 10-08-2010, 08:52 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi, Adam, Thanks. I didn't realize new...

Hi, Adam,
Thanks. I didn't realize new cufflnks can read bam. Now I am trying to see why UCSC genome browser can not read the bam file. Best, ldong
Forum: Bioinformatics 10-08-2010, 07:34 AM
Replies: 13
Views: 6,514
Posted By ldong
Hi, Bioinfo, I use bowtie for alignment. You...

Hi, Bioinfo,
I use bowtie for alignment. You can use samtools to convert different formats of alignments. Here is what I did. Best, ldong
...
Forum: Bioinformatics 10-08-2010, 07:29 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi adarob, Thank you for pointing to the right...

Hi adarob,
Thank you for pointing to the right direction. I downloaded new version tophat binary. Now it can read gtf file. I assume in this way, tophat will be more accurate. But when I compare...
Forum: Bioinformatics 10-07-2010, 11:35 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi, Pejman, I got the same error. To walk...

Hi, Pejman,
I got the same error. To walk around it I use the gtf file when I call cuffcompare. See our wiki site for detail:...
Forum: Bioinformatics 10-01-2010, 08:27 AM
Replies: 31
Views: 8,857
Posted By ldong
New version of tophat works!

New version of tophat works!
Forum: Bioinformatics 10-01-2010, 06:27 AM
Replies: 31
Views: 8,857
Posted By ldong
Hi, tguo, It looks like you don't have enough...

Hi, tguo,
It looks like you don't have enough reads as input. Please check how many reads are in your fastq file? To test cufflinks, I first used 1000 reads and got the same problem as yours....
Forum: Bioinformatics 06-08-2010, 08:36 AM
Replies: 278
Views: 118,528
Posted By ldong
Hi, Seb, Thank you very much for your...

Hi, Seb,

Thank you very much for your suggestions. Not sure if we can upgrade openmpi. I will check with system administrator.

We have a few nodes with 16 CPU and 64G memory allowing me to...
Forum: Bioinformatics 06-04-2010, 03:14 PM
Replies: 278
Views: 118,528
Posted By ldong
OpenMPI 1.2.8?

Hi Sebastien,
I followed the instruction in WiKi page and launched Ray about 20 hours ago. The processes are still running. Is this normal? When should it finish? I believe we have enough computing...
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