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Search: Posts Made By: Victory
Forum: Bioinformatics 07-20-2012, 04:21 PM
Replies: 1
Views: 1,909
Posted By Victory
Tophat library type and pair orientation for illumina data

I have some questions about read orientation in Tophat for Illumina data that I cannot find the clear answers yet and I hope you can shed some light on these.

1 Does the fr in...
Forum: Bioinformatics 07-16-2012, 12:20 PM
Replies: 0
Views: 1,915
Posted By Victory
library type parameter in Tophat for illumina data

I have some questions about read orientation in Tophat that I cannot find the clear answers yet and I hope you can shed some light on these.

1 What are the orientation of reads for pair-end data...
Forum: General 08-16-2011, 10:52 AM
Replies: 17
Views: 16,028
Posted By Victory
I think it should be okay Steven. Your link is...

I think it should be okay Steven. Your link is blocked for me and probably for others. I think you can remove that post to secure that no one can find the way to access it.
Forum: General 08-16-2011, 07:33 AM
Replies: 17
Views: 16,028
Posted By Victory
thank you very much Jim.

thank you very much Jim.
Forum: General 08-15-2011, 10:17 AM
Replies: 17
Views: 16,028
Posted By Victory
Are there anyway we can download raw read or the...

Are there anyway we can download raw read or the raw alignment not the graphical one?
Forum: General 11-26-2009, 08:10 AM
Replies: 9
Views: 25,097
Posted By Victory
Are there anyone have information about price of...

Are there anyone have information about price of sequencing per Mb for each platform? I got one from UCR website but it have only price for single end read. I also need information about pair end...
Forum: Bioinformatics 11-13-2009, 12:40 PM
Replies: 1
Views: 2,186
Posted By Victory
gap penalty in BWA

Hi,
I have short question about gap penalty in BWA. The manual said that the gap open penalty is 11 and gap extension penalty is 4. Does the first gap position will be charged 11 or 15?
Thank you
Forum: Bioinformatics 11-08-2009, 07:55 PM
Replies: 18
Views: 14,860
Posted By Victory
Thank you. I will try that.

Thank you. I will try that.
Forum: Bioinformatics 11-08-2009, 07:27 PM
Replies: 18
Views: 14,860
Posted By Victory
I use the import command to make BAM file. ...

I use the import command to make BAM file.
samtools import <in.ref_list> <in.sam> <out.bam>
Do I have to use specific command to install the SAM program or just put the program folder on the...
Forum: Bioinformatics 11-08-2009, 07:14 PM
Replies: 18
Views: 14,860
Posted By Victory
Thank you. I use SUN cluster computer. I have...

Thank you. I use SUN cluster computer. I have already copy whole folder of SAM version 0.1.6 to my working directory. However, it still doesn't work. I'm not sure which one is the install directory.
Forum: Bioinformatics 11-08-2009, 05:35 PM
Replies: 18
Views: 14,860
Posted By Victory
Install SAM tool

Are there anyone know how to install SAM tool? I read in the SAM document and it didn't say anything about that. Thank you.
Forum: Bioinformatics 11-08-2009, 07:54 AM
Replies: 2
Views: 1,333
Posted By Victory
OMG Thank you.

OMG Thank you.
Forum: Bioinformatics 11-07-2009, 05:06 PM
Replies: 2
Views: 1,333
Posted By Victory
BWA input problem

Hi,
I am a new user for BWA and I have problem with input file. I saw in the manual that I need to put arguement in <out.sai>in aln step and <in.sai> in samse step. I cannot distinguish between...
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