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Forum: Bioinformatics 07-16-2014, 12:54 AM
Replies: 2
Views: 800
Posted By sazz
Variance - basic statistics

Hello all,

I'm sorry for my very naive and basic question, but I am trying to understand a couple of graphs: dispersion, M vs A etc, and I am a little confused about "variance" term.

When you...
Forum: Bioinformatics 07-08-2014, 06:49 AM
Replies: 0
Views: 865
Posted By sazz
cuffcmp.combined.gtf vs. genes.gtf in CuffDiff

Hello all,

When I run CuffDiff with genes.gtf (annotation file I also used in Tophat2 when doing Transcriptome mapping) or cuffcmp.combined.gtf (generated by, cuffcompare -s...
Forum: RNA Sequencing 07-08-2014, 05:18 AM
Replies: 1
Views: 2,211
Posted By sazz
Hello Hyates, Depending on the output, I can...

Hello Hyates,

Depending on the output, I can say alpha is for q-value. But in the volcano plot it is the corresponding p-value. If your cutoff for q-value is 0.01 you should see that red dots for...
Forum: Bioinformatics 07-05-2014, 12:44 AM
Replies: 8
Views: 2,246
Posted By sazz
I updated my R version (3.1.0) and it works now....

I updated my R version (3.1.0) and it works now. Hope this helps..
Forum: Bioinformatics 07-04-2014, 03:46 AM
Replies: 8
Views: 2,246
Posted By sazz
Weird, 2 days ago I got the same error and I...

Weird, 2 days ago I got the same error and I thought I was doing something wrong, I hope it is about the version of R.
Forum: Bioinformatics 07-01-2014, 07:08 AM
Replies: 7
Views: 1,247
Posted By sazz
I tried to find the number of unique mappings...

I tried to find the number of unique mappings with "NH:i:1" tag but the result is exactly same as the number I find with MAPQ:50.

"-g 2": unique hits both with NH:i:1 and MAPQ 50 is 19,136,250...
Forum: Bioinformatics 07-01-2014, 05:45 AM
Replies: 7
Views: 1,247
Posted By sazz
yes, you are right. If you do a "-g 1" run, all...

yes, you are right. If you do a "-g 1" run, all the reads have MAPQ of 50, so it defines uniqueness depending on the output file.
Forum: Bioinformatics 07-01-2014, 05:32 AM
Replies: 7
Views: 1,247
Posted By sazz
Thanks to devon, I assume I could get the unique...

Thanks to devon, I assume I could get the unique hits from a default run (-g 20).

But to confirm if I get the unique hits, I performed several runs. So, if I substract
"-g 1" number of reads...
Forum: Bioinformatics 06-30-2014, 08:42 AM
Replies: 7
Views: 1,247
Posted By sazz
Unique mapping with Tophat2

Hello everyone,

I have seen posts about filtering unique hits after default run with Tophat2 but some say I should get the reads with MAPQ=255, some say I should get the reads with NH:i:1. Can you...
Forum: Bioinformatics 03-23-2014, 04:42 AM
Replies: 2
Views: 4,424
Posted By sazz
Solved, my files were not in Tab Delimited format...

Solved, my files were not in Tab Delimited format :/
Forum: Bioinformatics 03-23-2014, 04:20 AM
Replies: 2
Views: 4,424
Posted By sazz
Error at Creating Count Table for DESeq2

I have used Tophat-CuffDiff pipeline so far but I want to give a try for DESeq2. I have 2 conditions and 3 replicates for each, aim is to find the differentially expressed genes.

For a couple of...
Forum: Bioinformatics 03-15-2014, 10:29 AM
Replies: 26
Views: 9,610
Posted By sazz
Well, I have already made a comparison btw genome...

Well, I have already made a comparison btw genome and transcriptome mapping, while all the other parameters were exactly same.

First of all; in my experiment, I have control and target shRNA...
Forum: Bioinformatics 03-14-2014, 08:27 AM
Replies: 26
Views: 9,610
Posted By sazz
Dalesan, I would appreciate if you can share...

Dalesan,

I would appreciate if you can share your results, because I also wonder how much it differs when mapped on genome or transcriptome.
Forum: Bioinformatics 10-20-2013, 05:01 AM
Replies: 3
Views: 5,177
Posted By sazz
Hi yzzhang, I wrote to gsea developers,...

Hi yzzhang,

I wrote to gsea developers, that's the answer:

"The best approach would be to create a GCT file where rows are gene identifiers
(ideally, unique instances of human gene symbols),...
Forum: Bioinformatics 07-21-2013, 03:16 AM
Replies: 6
Views: 4,433
Posted By sazz
For me, I actually try different q cut-offs and...

For me, I actually try different q cut-offs and check the gene list output in DAVID to see which cutoff is giving more significant results; now for my last 2 RNA-seq exp. I am using q<0.01 cutoff but...
Forum: Bioinformatics 07-20-2013, 11:44 AM
Replies: 3
Views: 1,692
Posted By sazz
Thanks Gus, I am a little relieved.

Thanks Gus, I am a little relieved.
Forum: Bioinformatics 07-20-2013, 09:05 AM
Replies: 3
Views: 1,692
Posted By sazz
Cuffdiff p-value problem

Hello all,

I run the Tuxedo pipeline to find differentially expressed genes btw 2 phenotypes (3 replicates for each) but in the end I get p-values limited to "0.00005" in CuffDiff output, nothing...
Forum: Bioinformatics 07-20-2013, 08:44 AM
Replies: 3
Views: 1,159
Posted By sazz
Thanks DonDolowy, Graphpad worked well for me,...

Thanks DonDolowy, Graphpad worked well for me, and dpryan, I totally agree with you about R issue, I need to learn it if I will be using those kind of programs.
Forum: Bioinformatics 07-20-2013, 02:06 AM
Replies: 3
Views: 1,159
Posted By sazz
Plotting replicate FPKMs in log10

Hello everyone,

I have 2 phenotypes (knockdown vs. control) and 3 replicates for each of them. All mapped and cuffdiff-ed. I want to get a plot between my replicates from same phenotypes with FPKM...
Forum: Bioinformatics 07-15-2013, 09:44 AM
Replies: 1
Views: 1,256
Posted By sazz
What to do after finding differentially expressed genes?

Hello all,

Which programs do you use after finding the differentially expressed genes between 2 conditions? I assume, everyone first look at which GO terms are enriched. So far I have used DAVID,...
Forum: Bioinformatics 07-11-2013, 12:52 AM
Replies: 3
Views: 5,177
Posted By sazz
GSEA for RNA-seq data

Hello,

We have performed an RNA-seq analysis with Tuxedo Tools. There are 2 conditions and 3 replicates for each, and we have detected differentially expressed genes with 0.01 q cut-off.

Now,...
Forum: Bioinformatics 07-03-2013, 02:31 PM
Replies: 10
Views: 7,627
Posted By sazz
Output files should look like this: ...

Output files should look like this:

genes.read_group_tracking
genes.fpkm_tracking
genes.count_tracking
gene_exp.diff

I guess, you should delete ".tabular" part and organize them in the right...
Forum: Bioinformatics 07-03-2013, 03:58 AM
Replies: 7
Views: 5,867
Posted By sazz
Worked like a dream ! :) thanks GenoMax.

Worked like a dream ! :) thanks GenoMax.
Forum: Bioinformatics 07-03-2013, 03:41 AM
Replies: 7
Views: 5,867
Posted By sazz
I have unpacked them before and they are all in...

I have unpacked them before and they are all in .fastq format. I tried like you wrote, in the long form as:



Still give the same error:



But what I have realized is that; I have other...
Forum: Bioinformatics 07-03-2013, 03:22 AM
Replies: 7
Views: 5,867
Posted By sazz
I keep getting "-bash: *.fastq: Permission...

I keep getting "-bash: *.fastq: Permission denied" even though I have read - write and execute permissions (-rwxrwxrwx) :/ But thanks for the command, I will try to make it work.
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