SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 19 of 19
Search took 0.01 seconds.
Search: Posts Made By: nkwuji
Forum: Bioinformatics 11-23-2011, 05:19 AM
Replies: 6
Views: 2,824
Posted By nkwuji
Just a few examples as mentioned in my post. ...

Just a few examples as mentioned in my post.

Multivariate analysis package for microarray (clustering, PCA, COA ...)
Culhane AC, Thioulouse J, Perriere G, Higgins DG (2005) MADE4: an R package...
Forum: Bioinformatics 11-23-2011, 05:08 AM
Replies: 6
Views: 2,824
Posted By nkwuji
Hi, I am following the ml class. The...

Hi,

I am following the ml class. The techniques taught in the class are very useful in biology.

Actually until I took the class, I didnot realize that the techniques used in microarray data...
Forum: Bioinformatics 09-28-2011, 07:01 AM
Replies: 1
Views: 1,964
Posted By nkwuji
How to call SNP using known SNP information

Hi,

I am using samtools to call SNPs from RNA-seq data. I wonder whether I can use the known SNP frequency (or just the position of SNP) to improve my SNP calling. I know SOAPsnp can do that, but...
Forum: Bioinformatics 09-09-2011, 08:37 AM
Replies: 2
Views: 3,908
Posted By nkwuji
It seems something is wrong with the compilation...

It seems something is wrong with the compilation of the programs. After I recompile the programs using blimps following the instruction, most of the programs worked well (except...
Forum: Bioinformatics 09-05-2011, 08:05 AM
Replies: 2
Views: 3,908
Posted By nkwuji
Segmentation fault in sift4.03

Hi,

I recently came across the sift program. As I need to predict the effect of non-synonymous SNP on protein, I chose to use the sift sequence search...
Forum: RNA Sequencing 02-08-2011, 01:23 AM
Replies: 28
Views: 13,154
Posted By nkwuji
Hi, Lahoman, Here is the introduction for...

Hi, Lahoman,

Here is the introduction for cufflinks.
http://cufflinks.cbcb.umd.edu/manual.html

It is better to read through it. I thought there might be some shortcuts or easy ways to use it....
Forum: Bioinformatics 12-21-2010, 07:47 AM
Replies: 6
Views: 7,397
Posted By nkwuji
Hi, Lh3, Thx for your reply. Could you...

Hi, Lh3,

Thx for your reply. Could you elaborate it? I find an option in bcttools view

-P STR, type of prior: full, cond2, flat

Do you mean this option? What are the differences between...
Forum: Bioinformatics 12-21-2010, 06:35 AM
Replies: 6
Views: 7,397
Posted By nkwuji
Still unsolved... waiting for an answer...

Still unsolved... waiting for an answer...
Forum: Bioinformatics 12-14-2010, 02:16 AM
Replies: 6
Views: 7,397
Posted By nkwuji
Question on calling SNPs using samtools/bcftools

Hi,

I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is...
Forum: RNA Sequencing 11-26-2010, 05:19 AM
Replies: 28
Views: 13,154
Posted By nkwuji
Hi, Balat, Thx for sharing your experience....

Hi, Balat,

Thx for sharing your experience. That really helps. Actually I used a very similar protocol as you described, that I aligned all the reads from 7 lanes together using cufflinks, in...
Forum: RNA Sequencing 11-18-2010, 01:57 AM
Replies: 3
Views: 2,199
Posted By nkwuji
Hi, GKM, Thx for your reply. My library is...

Hi, GKM,

Thx for your reply. My library is Illumina RNA-seq. I just notice that there is an option in cufflinks of "--library-type", and the default setting is "fr-unstranded" for standard...
Forum: RNA Sequencing 11-15-2010, 08:08 AM
Replies: 3
Views: 2,199
Posted By nkwuji
cuffdiff for strand-unspecific sequencing

Hi,

I notice in my sequencing result that, the reads are not strand specific. There are lots of read matching the opposite strand of mRNA. There is a "--stranded=no" option in HTseq. But I didnot...
Forum: RNA Sequencing 11-15-2010, 02:47 AM
Replies: 15
Views: 16,606
Posted By nkwuji
It is a good practice to use juncs file instead....

It is a good practice to use juncs file instead. But for the last step in cufflinks--cuffdiff also requires a good GTF to calculate the geneexp.diff. So it is hard to get around the bad GTF.
Forum: RNA Sequencing 11-11-2010, 03:35 AM
Replies: 15
Views: 16,606
Posted By nkwuji
I fount the GTF file built by UCSC genome browser...

I fount the GTF file built by UCSC genome browser tends to have errors for stop_codon coordinates, then refused by cufflinks. This error was caused by some spliced stop_codons. I have tg write my own...
Forum: RNA Sequencing 11-03-2010, 02:01 AM
Replies: 3
Views: 2,365
Posted By nkwuji
Thx RockChalkJayhawk. I will think about...

Thx RockChalkJayhawk.

I will think about this part, though the result seems to be a little weird on genes expressed at low levels. For example, for this gene expressed in one sample with FPKM of...
Forum: RNA Sequencing 11-02-2010, 03:45 AM
Replies: 3
Views: 2,365
Posted By nkwuji
Binary characters in cuffcompare result & Questions on cuffdiff

Hi,

I am using tophat/cufflinks packages analyzing my RNA-seq data. I found a small bug in cuffcompare.

After I compared my reference gtf with transcript.gtf, I got the combined.gtf. But,...
Forum: Bioinformatics 10-28-2010, 06:04 AM
Replies: 31
Views: 8,495
Posted By nkwuji
I just read the script, it is very neat and...

I just read the script, it is very neat and clear. But I notice that you only count the assembled transcripts with "=" mark (match). How do you deal with transcripts with "c" mark (contained).
Forum: Bioinformatics 10-28-2010, 05:42 AM
Replies: 31
Views: 8,495
Posted By nkwuji
Hi, ldong, This is great. Thx a million. I...

Hi, ldong,

This is great. Thx a million. I will look into it.

Cheers,
Jun
Forum: Bioinformatics 10-28-2010, 03:51 AM
Replies: 31
Views: 8,495
Posted By nkwuji
Hi, In the tophat wiki page...

Hi,

In the tophat wiki page "https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/cufflinks-and-tophat#read", I found some very helpful perl scripts, for example,...
Showing results 1 to 19 of 19

 


All times are GMT -8. The time now is 09:01 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO