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Forum: Bioinformatics 03-11-2013, 07:41 AM
Replies: 0
Views: 914
Posted By shuang
How to convert hapmap file to QTL Cartographer format

I have hapmap data generated and I would like to run it through the QTL cartographer software. Are there any tools available to easily convert this data?
Forum: Bioinformatics 12-05-2012, 01:22 PM
Replies: 2
Views: 1,173
Posted By shuang
Segmentation fault from fastx_quality_stats

I was trying to generate a distribution of read quality and length of a fastq which was generated from PacBio.

I used "fastx_quality_stats" in fastx toolkit. However, I received error message of...
Forum: Bioinformatics 12-04-2012, 12:34 PM
Replies: 6
Views: 1,678
Posted By shuang
Thank you for your reply. I have 2 more...

Thank you for your reply. I have 2 more questions.

1. Does Quiver still need next-generation sequences for correction?

2. Any chance, by changing any parameters, I could reduce n in Celra?
Forum: Bioinformatics 12-04-2012, 11:46 AM
Replies: 6
Views: 1,678
Posted By shuang
Do yo mean use Quiver instead of celera ? ...

Do yo mean use Quiver instead of celera ?

Is Quiver a standard/common tool for assembling PacBio? (I'm new to PacBio)
Forum: Bioinformatics 12-03-2012, 09:24 AM
Replies: 6
Views: 1,678
Posted By shuang
'n' in PacBio assembled sequences?

I used Celera to assemble PacBio with correction with 454 sequences.

However, I found letter n (other than atcg) in the assembled result. Why ? and how do I fix it?
Forum: Bioinformatics 11-19-2012, 09:08 AM
Replies: 1
Views: 927
Posted By shuang
How to generate my own libarary for RepeatMasker

I want to generate my own library for RepeatMasker.

I plan to generate a library based on Plant Repeat Databases at Michigan State University...
Forum: Bioinformatics 10-26-2012, 10:54 AM
Replies: 10
Views: 4,369
Posted By shuang
I use Ubuntu. The in.txt is a fastq file, which...

I use Ubuntu. The in.txt is a fastq file, which was downloaded directly from the sequencing facility website.

17kb is the expected fully assembled length.
Forum: Bioinformatics 10-25-2012, 11:55 AM
Replies: 10
Views: 4,369
Posted By shuang
When I use -Q 33, it didn't go much further,...

When I use -Q 33, it didn't go much further, neither. Below is the command and the error message.
fastx_trimmer -i in.txt -Q 33 -o all.fastq


fastx_trimmer: Error: invalid quality score data on...
Forum: Bioinformatics 10-25-2012, 11:00 AM
Replies: 10
Views: 4,369
Posted By shuang
Sorry, I forgot to mention my sample is Illumina....

Sorry, I forgot to mention my sample is Illumina. The sample length is 17kb.
Forum: Bioinformatics 10-25-2012, 10:31 AM
Replies: 10
Views: 4,369
Posted By shuang
fastq_quality_trimmer error

I'm having problems in running commands of fastx tool. For example, when I ran fastx_trimmer,
fastx_trimmer -i in.txt -o out.fastq

I received this error
fastx_trimmer: Invalid quality score...
Forum: Bioinformatics 10-15-2012, 12:28 PM
Replies: 3
Views: 1,649
Posted By shuang
How to install Dotter in Linux

How to install Dotter in a Linux sever (Ubuntu)?

I found some source files from the site below. But then?

http://sonnhammer.sbc.su.se/download/software/dotter/
Forum: Bioinformatics 10-04-2012, 09:19 AM
Replies: 0
Views: 1,435
Posted By shuang
Error: BioPerl installation in Windows

I'm having problems in installing BioPerl on Windows 7.

I installed bioperl via PPM. My ActivePerl version is 5.16.1. It seemed PPM successfully installed packages listed below.

BioPerl 1.6.1...
Forum: Bioinformatics 08-27-2012, 11:14 AM
Replies: 1
Views: 2,129
Posted By shuang
Free software for ER diagrams

Could any one suggest a free software for generating ER diagrams?
Forum: Bioinformatics 07-18-2012, 11:29 AM
Replies: 1
Views: 1,085
Posted By shuang
promoter sequence analysis

I have about 100 promoter/5'UTR sequences. I would like to find out if any special motifs or TF biding sites among them. They are from Sorghum.

What would be a good tool or website for my purpose?
Forum: Bioinformatics 05-10-2012, 07:05 AM
Replies: 1
Views: 1,942
Posted By shuang
"Global median" function in R/Bioconductor?

Which function/package in R/Bioconductor can perform global median?

My input file is a txt separated by tab. My goal is to make/normalize each column to the same median.
Forum: Bioinformatics 05-07-2012, 12:31 PM
Replies: 1
Views: 1,677
Posted By shuang
how to use medpolish in R/Bioconductor

I'm trying to perform median polish on my RMA-normalized microarray data.

The function medpolish, which seem be able to perform median polish, outputs a matrix of factors. Am I supposedly use the...
Forum: Bioinformatics 04-14-2012, 01:19 PM
Replies: 1
Views: 1,051
Posted By shuang
R?bioconductor: how to generate an annotation library from a pgf or clf file

How to generate an annotation library from a pgf or clf file in R/Bioconductor?

I received a library folder from Affymatrix. It includes pgf, cif, clf, bgp, txt..... How do I generate a library...
Forum: Bioinformatics 04-14-2012, 07:27 AM
Replies: 1
Views: 1,332
Posted By shuang
How to load a new annotation from a local file to R/bioconductor

How to load a new annotation from a local file to R/Bioconductor?

I have a newly-created annotation library in my local server. How to I make R/Bioconductor use it? What kind of file format can a...
Forum: Bioinformatics 04-13-2012, 11:26 AM
Replies: 1
Views: 1,313
Posted By shuang
How to do median polish among three tables

I have 3 tables (derived from microarray datasets by gcrma normalization).

I want to perform "median polish" on these 3 tables. Basically, I want to make their median the same by proportionally...
Forum: General 03-19-2012, 12:55 PM
Replies: 1
Views: 1,482
Posted By shuang
can NOT connect to www.bioconductor.org

I need Bioconductor, preferred for windows. I'm having hard time to connect to www.bioconductor.org. Is there other sites where I can download Bioconductor?
Forum: Bioinformatics 03-08-2012, 08:42 AM
Replies: 2
Views: 3,049
Posted By shuang
After I set the path pointing to amos directory,...

After I set the path pointing to amos directory, the problem was solved. Thanks!
Forum: Bioinformatics 03-08-2012, 08:30 AM
Replies: 0
Views: 1,006
Posted By shuang
super-structures centromeric repeats

I'm trying to analyze super-structures (higher-order) of satellite repeats in centromere region. I've retrieved 55 copies of satellite (136bp) homologous repeats via crossmatch.

Next, how do I...
Forum: Bioinformatics 02-27-2012, 11:05 AM
Replies: 0
Views: 882
Posted By shuang
How to upgrade Minimus to Minimus2

I have amos-3.1.0 on my server. Minimus is part of the package. If I want to run Minimus2 instead, how can I upgrade the software?
Forum: Bioinformatics 02-24-2012, 01:20 PM
Replies: 2
Views: 1,864
Posted By shuang
tools for assembling large contigs

I need a tool to assemble very large reads.

I have 2 sets of large contigs, from 454 and Pacbio. The largest contig is 20kb. The average length is 4kb. I'm trying to use those 2 sets of contigs in...
Forum: Bioinformatics 02-20-2012, 09:26 AM
Replies: 17
Views: 9,965
Posted By shuang
problems in installing AMOS

I'm trying to make amos-3.1.0 work on Ubuntu. When I ran ./configure, it gave me a warning in the end

WARNING! Qt4 toolkit malfunctioning but is required to run AMOS GUIs
try compiling GUIs...
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