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Forum: Bioinformatics 12-04-2015, 05:27 PM
Replies: 2
Views: 1,414
Posted By liux
any suggestion?

any suggestion?
Forum: Bioinformatics 12-03-2015, 09:39 AM
Replies: 2
Views: 1,414
Posted By liux
Question ribosomal genes in differentially expressed gene list

a lab with partially degraded mRNAseq samples came back with a list of DE genes. And there are a few ribosomal protein genes in the list, which are not supposed to be there. How did this happen, and...
Forum: Academic/Non-Profit Jobs 10-26-2015, 12:27 PM
Replies: 0
Views: 800
Posted By liux
Bioinformatics data analyst - comparative, evolutionary analysis; NGS analysis

https://www.ohr.wisc.edu/Weblisting/External/PVLSummaryPrint.aspx?pvl_num=83932

Working Title:
DATA ANALYST
Official Title:
RESEARCHER(E05DN) or ASSOC RESEARCHER(E05FN) or ASST...
Forum: Bioinformatics 05-05-2015, 11:40 AM
Replies: 1
Views: 2,462
Posted By liux
stringtie output has exons instead of transcript annotation

Hi,

has anyone used stringtie program? I have a genome annotation that mostly has one isoform annotated per gene. I tried to use stringtie to see if it can help get more transcript annotated....
Forum: RNA Sequencing 03-15-2015, 05:46 PM
Replies: 1
Views: 1,567
Posted By liux
irap installation error - cpanm: command not found

When I install currentl version of iRAP (0.6.0p4) on centos 6.5, I got following error:

[INFO] Installing perl packages...
[INFO] Package Algorithm::Munkres
./irap/scripts/irap_install.sh: line...
Forum: Bioinformatics 11-15-2014, 07:20 AM
Replies: 1
Views: 2,543
Posted By liux
Lightbulb Transcription Start Sites (TSS) analysis for 5' RNAseq data

I recently start working on a TSS analysis project (yeast). And want to get some suggestions.

The experiment had mRNA from two population of yeast sequenced on 5' only. The goal is to detect the...
Forum: Bioinformatics 11-11-2014, 02:46 PM
Replies: 4
Views: 1,475
Posted By liux
whole genome metagenomics - longer reads or more reads

From data analysis point of view, if you had the option of 4 lanes of sequencing at 2x100 bp, or 3 lanes of sequencing at 2x150 bp, and you were trying to assemble a whole genome metagenomic sample,...
Forum: Bioinformatics 10-23-2014, 09:35 AM
Replies: 1
Views: 881
Posted By liux
is rpy2-bioconductor-extensions good? is it still up to date?

My primary scripting language is python. And I start to use R packages more often, but still prefers working in python.

I start to look into rpy2, also noticed rpy2-bioconductor-extensions. But...
Forum: Bioinformatics 09-16-2014, 09:06 AM
Replies: 4
Views: 3,742
Posted By liux
Thanks for the reply. These are exactly...

Thanks for the reply.

These are exactly what I thought, and recommended to the researcher. Unfortunately I have no control over how the sequencing was designed. But I can refuse to performed the...
Forum: Bioinformatics 09-15-2014, 07:04 PM
Replies: 4
Views: 3,742
Posted By liux
genome assembly with only mate pair reads

Hi,

I am mostly comfortable with DNA resequencing, mRNAseq, ChIPseq, etc. data. And always feel difficult handling de novo assembly works. But it comes my way anyway.

I have a set of data that...
Forum: Bioinformatics 07-15-2013, 08:42 AM
Replies: 7
Views: 3,594
Posted By liux
If you have to, use subprocess package. It should...

If you have to, use subprocess package. It should work fine.

I think shell script is straightforward, and should be used, if all it does is to run a simple command. But I prefer python when the...
Forum: Bioinformatics 03-02-2013, 10:09 AM
Replies: 5
Views: 2,095
Posted By liux
We mask all but one copy if the duplicates are...

We mask all but one copy if the duplicates are exactly the same (~50% of genes) or less than 1% (other 40%); and flag the rest.

It is probably OK if just looking at the gene expression. recently...
Forum: Academic/Non-Profit Jobs 07-10-2012, 12:32 PM
Replies: 0
Views: 1,648
Posted By liux
Bioinformaticist position at University of Wisconsin Biotechnology Center

UWBC bioinformaticist position (http://www.ohr.wisc.edu/pvl/pv_074054.html)

UNIVERSITY OF WISCONSIN-MADISON
Position Vacancy Listing
PVL# 74054
Working title:
BIOINFORMATICIST

Official...
Forum: Bioinformatics 12-09-2011, 01:56 PM
Replies: 12
Views: 8,778
Posted By liux
Any progress on this? would love to see how other...

Any progress on this? would love to see how other people does mRNAseq variants calling with TopHat output.
Forum: Illumina/Solexa 11-04-2011, 07:46 AM
Replies: 2
Views: 2,324
Posted By liux
We did. And they told us how to modify the...

We did. And they told us how to modify the config.xml file. And that is how we modified the config.xml from a 75bp run.

after posting this yesterday, I further examined the config.xml from that...
Forum: Illumina/Solexa 11-03-2011, 01:13 PM
Replies: 2
Views: 2,324
Posted By liux
Help!! need a copy of config.xml file from GAIIx run

Hi,

I need a copy of config.xml from a 100bp, single reads, GAIIx run (<runfolder>/Dana/Intensity/BaseCalls/config.xml)

a lab in the campus acquired a GAIIx machine. After the first run, they...
Forum: Bioinformatics 11-03-2011, 01:03 PM
Replies: 9
Views: 3,624
Posted By liux
I would recommend python for anyone new in...

I would recommend python for anyone new in Bioinformatics too. if you already knew perl, there is no need to switch. But if you are totally new, python is a cleaner language, easier to learn, but is...
Forum: Bioinformatics 03-01-2011, 01:28 PM
Replies: 4
Views: 2,348
Posted By liux
My institute does not have subscription to the...

My institute does not have subscription to the journal anymore. Maybe because most articles are open-access. :sigh:

a free trial does grant me access to it. but only good for 30 days.
Forum: Bioinformatics 12-22-2010, 03:13 PM
Replies: 8
Views: 3,974
Posted By liux
In my case (maybe very special), there are a...

In my case (maybe very special), there are a couple dozen out of all genes are of interests. so, to output only the specific exons is often requested.
Forum: Bioinformatics 12-22-2010, 12:45 PM
Replies: 8
Views: 3,974
Posted By liux
this is very nice feature. But it seems that it...

this is very nice feature. But it seems that it can only output one region at a time?

I am wondering if the pileup can be made according to a BED file or any files that defines a series of...
Forum: Bioinformatics 11-16-2010, 10:18 AM
Replies: 3
Views: 2,622
Posted By liux
found a solution in the manual. since erange...

found a solution in the manual. since erange assumes two neighoring exons from one gene should be with in 20kb, the maximum 'insert' between a pair can be set by -X option, which is 20300 for this...
Forum: Bioinformatics 11-15-2010, 03:02 PM
Replies: 3
Views: 2,622
Posted By liux
The intention is to compare how well different...

The intention is to compare how well different mRNAseq tools perform with a common dataset. ERANGE is one in the list, and ERANGE will use bowtie alignment. I could just use bowtie to align those as...
Forum: Bioinformatics 11-15-2010, 12:19 PM
Replies: 3
Views: 2,622
Posted By liux
use bowtie for paired-end mRNA-seq reads?

I am trying to map 10 million pairs of reads to the genome + splice junction templates. However Bowtie will not align most of the reads.

here is the command I used and the screen output (partial):...
Forum: General 10-12-2010, 12:05 PM
Replies: 10
Views: 8,122
Posted By liux
try wise2:...

try wise2: http://www.ebi.ac.uk/Tools/Wise2/index.html
Forum: Bioinformatics 08-24-2010, 10:48 AM
Replies: 1
Views: 3,819
Posted By liux
However, when I run lanes individually, no...

However, when I run lanes individually, no problems were reported at all.

Anyone know the cause of the error?

right now, I am align lanes individually, and plan to merge, sort and index them...
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