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Search: Posts Made By: ptong7
Forum: Bioinformatics 09-07-2011, 02:21 PM
Replies: 9
Views: 3,950
Posted By ptong7
tophat-fusion error

Hi guys,

is anybody use tophat-fusion?
I use 'tophatfusion-0.1.0-OSX_x86_64' ran my RNA-seq data get some error like:

Traceback (most recent call last):
File...
Forum: Bioinformatics 06-07-2010, 08:47 AM
Replies: 1
Views: 2,402
Posted By ptong7
help, the SOAPsnp input files format

Hi all,
Is anyone familiarity with SOAPsnp input files?

My alignment file is sam file. I want to use SOAPsnp call SNP.
Is anybody know how to convert the sam file to the SOAPsnp input files?
...
Forum: Bioinformatics 12-23-2009, 12:22 PM
Replies: 0
Views: 5,680
Posted By ptong7
SNP mapping quality problem

Hi everyone,

I use glfProgs package calling SNP.
And at the output file, the 5th column is Phred-like consensus quality.
Is anyone can tell me how to calculate the consenses mapping quality (...
Forum: Bioinformatics 07-30-2009, 03:32 AM
Replies: 4
Views: 1,483
Posted By ptong7
Thanks nilshomer, It works...

Thanks nilshomer, It works...
Forum: Bioinformatics 07-28-2009, 08:52 AM
Replies: 4
Views: 1,483
Posted By ptong7
Hi nilshomer, I try "samtools view -x...

Hi nilshomer,
I try "samtools view -x aln.sorted.bam <region>".
but I got this "view: illegal option -- x"
Forum: Bioinformatics 07-28-2009, 06:57 AM
Replies: 4
Views: 1,483
Posted By ptong7
SAM file flag problem

Hi all,
Is any body know what's the the flag means in the SAM file.
The Flag I got looks different with the SAM manual.

Thanks!

Here is a sample of my sam file.
...
Forum: Illumina/Solexa 05-19-2009, 04:26 AM
Replies: 1
Views: 1,351
Posted By ptong7
Question detect SVs

Hi all,
Is anybody use maq.pl script "sv" function to detect SVs?
Is that good?

cheers,
Forum: Illumina/Solexa 04-07-2009, 01:33 PM
Replies: 0
Views: 1,431
Posted By ptong7
Unhappy Gbrowse problem???

Hi everyone,

Is anybody use GBrowse can do me a favour?
Toady I install GBrowse in my MAC pro. I think it's already install succeed.
But when I open "http://localhost/gbrowse" to test the...
Forum: Illumina/Solexa 12-01-2008, 05:46 PM
Replies: 2
Views: 2,269
Posted By ptong7
maqview

hi everyone:
I already contact with the author who write the MAQ.
Now I know why I canít open the map file in Maqview.
The MAQ, which I used was too new to the Maqview. If use the MAQ-0.6.8, I...
Forum: Illumina/Solexa 10-30-2008, 02:26 AM
Replies: 2
Views: 2,269
Posted By ptong7
analyse illumina data

hi everyone,
i already got the illumina sequencing data, and i run the data on the MAQ.
now i have the result data as xxx.map file.
I dont know how to show the result on the browser .

is there...
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