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Search: Posts Made By: kenosaki
Forum: Genomic Resequencing 04-02-2013, 09:42 PM
Replies: 2
Views: 2,233
Posted By kenosaki
I found that MALBAC (Multiple Annealing and...

I found that MALBAC (Multiple Annealing and Looping Based Amplification Cycles; PMID 23258894) may be an alternative method :)
Forum: Genomic Resequencing 04-01-2013, 04:55 PM
Replies: 2
Views: 2,233
Posted By kenosaki
Post Whole Genome Amplification for Cancer Study

Id like to sequence the tumor sample that material is very limited amount. My goal is to find a structural variant like large inversion and deletion (translocation if possible) in a single tumor...
Forum: RNA Sequencing 10-12-2011, 03:41 AM
Replies: 1
Views: 2,972
Posted By kenosaki
RPKM and expression comparison

When you use RPKM for expression value and want to compare the value of multiple genes, what are the things you should be careful with?

Theoretically, RPKM is normalized expression value which...
Forum: Bioinformatics 08-29-2011, 08:15 PM
Replies: 2
Views: 2,389
Posted By kenosaki
Thanks vebaev, Do you use Deseq for miRNA...

Thanks vebaev,
Do you use Deseq for miRNA expression analysis?
One of my concern is the number of miRNA I have in my list is small, 300 ~ 800, depending on a category.
Can I assume that most of...
Forum: Bioinformatics 08-29-2011, 07:20 AM
Replies: 2
Views: 2,389
Posted By kenosaki
microRNA normalization

Hi,

Does anyone know the reasonable normalization methods for microRNA data analysis?
I already trimmed adaptor, mapped these reads to the reference, and counted the number of reads that mapped...
Forum: Bioinformatics 06-24-2011, 03:12 AM
Replies: 5
Views: 1,740
Posted By kenosaki
Thanks volks, This is an Illumina GAIIx data. ...

Thanks volks,
This is an Illumina GAIIx data.
I just want to know if i need to add or change some parameters based on the read length.
Do I use the same command-line for 80 bp reads mapping as I...
Forum: Bioinformatics 06-24-2011, 01:17 AM
Replies: 5
Views: 1,740
Posted By kenosaki
bowtie 80 mer-long mapping

Hi,

I try to map relatively long reads (80-bases-long single read, fastq format) to hg19 using bowtie.
Does anybody tell me which parameters should be modify for this kind of mapping ?
I used...
Forum: Bioinformatics 05-31-2011, 11:19 PM
Replies: 31
Views: 12,454
Posted By kenosaki
Thanks Anelda, I'll check this thread...

Thanks Anelda, I'll check this thread...
Forum: Bioinformatics 05-31-2011, 05:41 PM
Replies: 31
Views: 12,454
Posted By kenosaki
And my command is this. cuffmerge -g...

And my command is this.

cuffmerge -g ../bowtie_work/bowtie_ref/refGene.gtf -s ../bowtie_work/bowtie_ref/hg19.fa assemblies.txt
Forum: Bioinformatics 05-31-2011, 05:40 PM
Replies: 31
Views: 12,454
Posted By kenosaki
Hi, does anyone have experienced the error when...

Hi, does anyone have experienced the error when running caffmerge?
I think merge file has no problem.
Cufflinks was run using a sorted bam file, and I have three cufflinks results.

And my...
Forum: Bioinformatics 03-02-2011, 11:15 PM
Replies: 7
Views: 4,649
Posted By kenosaki
Thanks guys, I'll try them.

Thanks guys, I'll try them.
Forum: Bioinformatics 02-28-2011, 04:17 PM
Replies: 7
Views: 4,649
Posted By kenosaki
That's what I thought at first, but I'm not sure...

That's what I thought at first, but I'm not sure where I should split the read out. As you know, the first half has higher quality than the last half has.

But thanks, bowtie could be my option.
Forum: Bioinformatics 02-28-2011, 01:18 AM
Replies: 7
Views: 4,649
Posted By kenosaki
Gene fusion detection

Hi,
I am wondering if detection of fusion gene is possible using a GA's single but relatively long (70-100 bp) read RNA-Seq data.
I know some software can detect fusion gene from paired-end...
Forum: General 02-18-2011, 11:08 PM
Replies: 7
Views: 3,994
Posted By kenosaki
You mean, comparing the peaks of two libraries...

You mean, comparing the peaks of two libraries without input control?
Forum: General 01-16-2011, 10:52 PM
Replies: 6
Views: 2,505
Posted By kenosaki
thanks guys for usuful information. jbrowse is...

thanks guys for usuful information.
jbrowse is looks nice.
Forum: General 01-11-2011, 01:19 AM
Replies: 6
Views: 2,505
Posted By kenosaki
Looking for a NGS viewer in iPad

Does anyone know any viewers compatible to iPad?
Free application would be better, but commercial viewer is also OK if there is no freeware.

I want to show .wig or .bed in the viewer using my...
Forum: Bioinformatics 10-21-2010, 08:58 PM
Replies: 14
Views: 3,164
Posted By kenosaki
I sent the conf file to you by e-mail. Locate...

I sent the conf file to you by e-mail. Locate this file into the libray folder of expression console :)
I suggest that you delete your e-mail address from this thread now.

By the way, exon level...
Forum: Bioinformatics 10-21-2010, 12:57 AM
Replies: 14
Views: 3,164
Posted By kenosaki
Question 1, A: Probeset ID is unique, as long...

Question 1,
A: Probeset ID is unique, as long as of the same chip. I don't think there is a change on different version. Every probe was designed from a transcript cluster (RefSeq RNA, EST,etc), so...
Forum: Bioinformatics 10-20-2010, 07:23 PM
Replies: 14
Views: 3,164
Posted By kenosaki
Ok, you can get CEL file. I usually download the...

Ok, you can get CEL file. I usually download the CEL file when I want to probe level signals.
I like Expression Console...
Forum: Bioinformatics 10-20-2010, 04:55 PM
Replies: 14
Views: 3,164
Posted By kenosaki
What data set did you download from? Tell us GEO...

What data set did you download from? Tell us GEO accession # and downloaded dataset. It may help us to tell you how to get expression value.
Forum: RNA Sequencing 08-26-2010, 06:15 AM
Replies: 3
Views: 4,395
Posted By kenosaki
yes, this thread helps a lot. Thanks Steven

yes, this thread helps a lot.

Thanks Steven
Forum: RNA Sequencing 08-25-2010, 11:13 PM
Replies: 3
Views: 4,395
Posted By kenosaki
RNA-Seq without reference

Hi
Does anyone try transcriptome analysis of the organism of which reference genome is unknown?
The organism is plant, and have about 80 % similarity of Arabidopsis genes at nucleotide level. ...
Forum: RNA Sequencing 08-08-2010, 11:15 PM
Replies: 1
Views: 2,201
Posted By kenosaki
Smile Allelic imbalance and expression

Hi,

Does anyone know the method or tools to find the region of allelic imbalance in RNA-Seq transcripts?

I read one paper
Tumor transcriptome sequencing reveals allelic expression imbalances...
Forum: RNA Sequencing 08-04-2010, 01:06 AM
Replies: 4
Views: 3,035
Posted By kenosaki
Thank you Simon, I found the very...

Thank you Simon,

I found the very informative thread about RPKM.
http://seqanswers.com/forums/showthread.php?t=3254

Ken
Forum: RNA Sequencing 07-11-2010, 05:38 PM
Replies: 4
Views: 3,035
Posted By kenosaki
I'd like to look at, 1) Global expression...

I'd like to look at,
1) Global expression changes of genes between two groups of sample from different tissues. (like microarray experiment)
2) The exons that specifically spliced in the...
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