SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 48
Search took 0.00 seconds.
Search: Posts Made By: wilson90
Forum: Bioinformatics 12-18-2016, 10:03 PM
Replies: 0
Views: 1,279
Posted By wilson90
deLaat's 4Cseqpipe

Hi,

I have tried a few times to download the source files for 4Cseqpipe and references from Tanay, de Laat's website.

Have anyone been able to either wget/curl the links such as...
Forum: Bioinformatics 06-30-2015, 09:56 PM
Replies: 1
Views: 678
Posted By wilson90
This is the part where the author tries to...

This is the part where the author tries to estimate copy number. It is kind of him to share his code, but it comes without any comment or explanation.

Can anyone familiar with CNV field kind...
Forum: Bioinformatics 06-30-2015, 06:36 PM
Replies: 1
Views: 678
Posted By wilson90
Have anyone tried analysis in Baslan 2012 "Genome-wide CNV analysis of Single-cell"?

Hi All,

I have been trying to use the analysis flow suggested by the paper, but it seems like I am not getting it. Just a show of hand if anyone of you have successfully replicated the analysis...
Forum: Bioinformatics 02-15-2015, 02:03 AM
Replies: 0
Views: 1,173
Posted By wilson90
Relative STrand Cross-correlation coefficient (RSC) negative value???

Hi All,

I am trying to obtain the RSC value using Phantompeakqualtool on my single-end 50bp ChIP-seq data. No replicate. However, I realize that I am getting a very strange RSC value. It is...
Forum: Bioinformatics 11-02-2014, 05:57 PM
Replies: 0
Views: 709
Posted By wilson90
Running SICER on rn5

hi,

I am trying to run SICER on rn5, but it returns an error saying "this genome is not recognized". Have someone overcome this genome assembly issue with SICER before?

Thank you.

Best...
Forum: Bioinformatics 10-20-2014, 12:06 AM
Replies: 0
Views: 707
Posted By wilson90
spliceR runtime

Hi,

Can anyone share with me what is the usual runtime for spliceR? For me, on a SMP, it is running for 2 hours already. (total number of samples 10)

Best Regards,
Wilson
Forum: Bioinformatics 09-30-2014, 07:23 PM
Replies: 1
Views: 1,007
Posted By wilson90
repbase data for mouse/rat/chicken

Hi all,

I am a newbie in dealing with repeated elements. I have read a lot of methylation studies which use Repbase for repeated element analysis (especially in human). I wonder if Repbase dataset...
Forum: Bioinformatics 08-06-2014, 06:00 PM
Replies: 649
Views: 170,713
Posted By wilson90
Hi. I am just wondering if it is advisable to...

Hi. I am just wondering if it is advisable to merge bam files produced by Bismark using samtools merge, and then run methyl_extrator?

The reason why I am asking this question is because I have...
Forum: RNA Sequencing 03-02-2014, 06:54 PM
Replies: 20
Views: 10,330
Posted By wilson90
Just wondering, what is a geneset file? How do...

Just wondering, what is a geneset file?
How do you define the geneset file?
Any example format?
Thank you.
Forum: Bioinformatics 01-05-2014, 10:03 PM
Replies: 92
Views: 36,078
Posted By wilson90
In your vignette, we are suppose to provide our...

In your vignette, we are suppose to provide our annotation file.
I wonder where have you obtained "kegg.gs"?
and I want to use GO annotation. So where can I obtain "GO.gs" in R?
Thank you.
...
Forum: Bioinformatics 10-07-2013, 02:02 AM
Replies: 1
Views: 1,270
Posted By wilson90
Smile PCA analysis

Dear all,

I would like to use PCA to do initial subtyping of my RNA-Seq samples. But, I have questions regarding the loadings value (using prcomp in R).

It is fine if my loadings values for...
Forum: Bioinformatics 09-18-2013, 12:06 AM
Replies: 10
Views: 3,219
Posted By wilson90
Interesting Indeed

I have played with some data, and generated some data. Theoretically, it should be a "pristine" dataset.

I wonder if cuffdiff2 is as robust when it comes to single-cell rna-seq data?
Forum: Bioinformatics 09-18-2013, 12:05 AM
Replies: 10
Views: 3,219
Posted By wilson90
Interesting Indeed

I have played with some data, and generated some data. Theoretically, it should be a "pristine" dataset.

I wonder if cuffdiff2 is as robust when it comes to single-cell rna-seq data?
Forum: Bioinformatics 09-17-2013, 06:04 PM
Replies: 10
Views: 3,219
Posted By wilson90
Are all existing softwares on RNA-Seq analysis still useful for Single-Cell RNA-Seq?

Dear all,

I am currently pursuing my interest in Single-Cell transcriptomics, but I worry that the statistical model optimized for rna-seq might not be applicable to Single-cell or Single-nuclei...
Forum: Bioinformatics 08-29-2013, 05:18 PM
Replies: 0
Views: 1,185
Posted By wilson90
Cuffdiff-2.1.1 Segmentation Fault at Differential Expression Analysis Stage

Dear all,

What is wrong with cuffdiff-2.1.1? It keeps returning Segmentation Fault in this run, while "boost::thread_resource_error" in the other run.

Nonetheless, I have to get my job done. ...
Forum: Bioinformatics 08-19-2013, 01:38 AM
Replies: 5
Views: 1,531
Posted By wilson90
for more info: ##Trimming Low Qual reads and...

for more info:

##Trimming Low Qual reads and Bases with low quality
java -jar Trimmomatic-0.30/trimmomatic-0.30.jar PE -phred33 read_1.fq read_2.fq output_forward_paired.fq.gz...
Forum: Bioinformatics 08-19-2013, 01:34 AM
Replies: 5
Views: 1,531
Posted By wilson90
Would it be because: 1. Annotation issue? 2....

Would it be because:
1. Annotation issue?
2. I remove duplicative reads using picard?
3. Library issue ( among biological replicates)?
4. I have performed upper-quartile normalization in...
Forum: Bioinformatics 08-19-2013, 01:32 AM
Replies: 5
Views: 1,531
Posted By wilson90
cuffdiff -o bam_noslash -b $GENOME -p 35 -L G1,G2...

cuffdiff -o bam_noslash -b $GENOME -p 35 -L G1,G2 -N -u merged_asm/merged.gtf $BAM1,$BAM2,$BAM3,$BAM4,$BAM5,$BAM6,$BAM7,$BAM8,$BAM9,$BAM10...
Forum: Bioinformatics 08-18-2013, 07:21 PM
Replies: 5
Views: 1,531
Posted By wilson90
This is what worries me.

> Processed 28454 loci. [*************************] 100%
Performed 0 isoform-level transcription difference tests
Performed 0 tss-level transcription difference tests...
Forum: Bioinformatics 08-16-2013, 11:38 PM
Replies: 5
Views: 1,531
Posted By wilson90
cuffdiff uses bam file or Sam file

Just wondering if cuffdiff uses Sam file or bam file as input.

The reason for my post is because in my previous run, the output of cuffdiff says no differential expression is performed on my...
Forum: Bioinformatics 08-15-2013, 08:03 PM
Replies: 1
Views: 867
Posted By wilson90
FastQC output: Do I trim these?

I am looking at the per base quality score of my RNA-Seq data, and found that the quality looks great. (as attached)

But when I look at the per base sequence, the first 10 bases seems to be...
Forum: Bioinformatics 08-14-2013, 06:59 PM
Replies: 1
Views: 1,810
Posted By wilson90
Generally Applicable Gene-set Analysis (GAGE) problem

I am trying to use GAGE to do some pathway analysis based on RNA-Seq data. The vignette is nicely written, but there is an error that I do not know if it is my fault in my script.

I will show you...
Forum: Bioinformatics 07-30-2013, 01:07 AM
Replies: 0
Views: 660
Posted By wilson90
Cuffdiff and Cufflink Error with -g option?

Dear all,

I am using cufflink to produce transcript abundance level estimation, and cuffdiff to do differential analysis.

However, I have come across this contradiction that certain genes,...
Forum: Bioinformatics 07-07-2013, 11:50 PM
Replies: 1
Views: 1,058
Posted By wilson90
Determine Top 100 Differentially Expressed Genes

Dear all,

I am wondering if we decide the top 100 differentially expressed genes based on:
A) Log Fold Change or
B) P-value
C) Or a combination them? (In the case, order matters? (logFC first,...
Forum: RNA Sequencing 07-02-2013, 10:53 PM
Replies: 20
Views: 10,330
Posted By wilson90
I am sorry, but it is not available for R version...

I am sorry, but it is not available for R version 2.15.1. Is it still available?
Showing results 1 to 25 of 48

 


All times are GMT -8. The time now is 05:55 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO