Forum: Bioinformatics
11-23-2011, 06:19 AM
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Replies: 6
Views: 2,918
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...
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Forum: Bioinformatics
11-23-2011, 06:08 AM
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Replies: 6
Views: 2,918
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...
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Forum: Bioinformatics
09-28-2011, 08:01 AM
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Replies: 1
Views: 2,041
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...
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Forum: Bioinformatics
09-09-2011, 09:37 AM
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Replies: 2
Views: 4,032
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Forum: Bioinformatics
09-05-2011, 09:05 AM
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Replies: 2
Views: 4,032
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...
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Forum: RNA Sequencing
02-08-2011, 02:23 AM
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Replies: 28
Views: 13,457
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....
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Forum: Bioinformatics
12-21-2010, 08:47 AM
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Replies: 6
Views: 7,519
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...
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Forum: Bioinformatics
12-21-2010, 07:35 AM
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Replies: 6
Views: 7,519
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Forum: Bioinformatics
12-14-2010, 03:16 AM
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Replies: 6
Views: 7,519
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...
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Forum: RNA Sequencing
11-26-2010, 06:19 AM
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Replies: 28
Views: 13,457
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...
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Forum: RNA Sequencing
11-18-2010, 02:57 AM
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Replies: 3
Views: 2,292
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...
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Forum: RNA Sequencing
11-15-2010, 09:08 AM
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Replies: 3
Views: 2,292
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...
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Forum: RNA Sequencing
11-15-2010, 03:47 AM
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Replies: 15
Views: 16,850
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Forum: RNA Sequencing
11-11-2010, 04:35 AM
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Replies: 15
Views: 16,850
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Forum: RNA Sequencing
11-03-2010, 03:01 AM
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Replies: 3
Views: 2,465
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...
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Forum: RNA Sequencing
11-02-2010, 04:45 AM
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Replies: 3
Views: 2,465
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Forum: Bioinformatics
10-28-2010, 07:04 AM
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Replies: 31
Views: 8,814
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).
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Forum: Bioinformatics
10-28-2010, 06:42 AM
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Replies: 31
Views: 8,814
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Forum: Bioinformatics
10-28-2010, 04:51 AM
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Replies: 31
Views: 8,814
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,...
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