Forum: Bioinformatics
02-19-2015, 06:07 AM
|
|
Replies: 8
Views: 1,719
Yeah, I already got it to work with bed tools...
Yeah, I already got it to work with bed tools closestBed command. Only issue was with type of text editor I was using to generate .bed file as I described for anyone else having similar issues.
|
|
Forum: Bioinformatics
02-19-2015, 05:52 AM
|
|
Replies: 8
Views: 1,719
|
|
Forum: Bioinformatics
02-13-2015, 12:57 PM
|
|
Replies: 8
Views: 1,719
I did as "sarvidsson" suggested
Both files...
I did as "sarvidsson" suggested
Both files contain chromosome name, start position, stop position, and name of feature/gene without headings
Here is an example
My list of 400 position are in...
|
|
Forum: Bioinformatics
02-10-2015, 12:14 PM
|
|
Replies: 8
Views: 1,719
|
|
Forum: Bioinformatics
02-10-2015, 12:11 PM
|
|
Replies: 8
Views: 1,719
Promoter Analysis
I did ChIP-seq on a TF.
Now I have a consensus binding site. ATGNNNCGCNNNCAT (whatever)
What I want to do is predict where else this consensus binding site is aside from the ChIP sites. I used...
|
|
Forum: General
08-18-2014, 11:52 AM
|
|
Replies: 6
Views: 1,961
This is regarding my original question.
...
This is regarding my original question.
What If I find consensus sequences in that region yet still no differential gene expression. So the consensus would imply that this site is preferred by...
|
|
Forum: General
08-15-2014, 10:27 AM
|
|
Replies: 6
Views: 1,961
ChiP-seq and RNA-seq
I was wondering if anyone has done both ChIP-seq and RNA-seqand observed that while you have a DNA binding site inside the gene or on the promoter region of a gene, but the gene expression did not...
|
|
Forum: Sample Prep / Library Generation
05-08-2014, 07:12 AM
|
|
Replies: 23
Views: 36,098
|
|
Forum: Sample Prep / Library Generation
05-07-2014, 03:20 PM
|
|
Replies: 23
Views: 36,098
|
|
Forum: Bioinformatics
04-27-2014, 12:57 PM
|
|
Replies: 6
Views: 3,593
|
|
Forum: Bioinformatics
04-27-2014, 12:39 PM
|
|
Replies: 6
Views: 3,593
So i ran this an I got the wrong counts
The...
So i ran this an I got the wrong counts
The numbers are just off... the start and stop bases match everything looks good but the % is off...
A + G + T + C = correct lengths per gene but the...
|
|
Forum: Bioinformatics
04-25-2014, 03:02 PM
|
|
Replies: 14
Views: 2,333
|
|
Forum: Bioinformatics
04-25-2014, 02:55 PM
|
|
Replies: 14
Views: 2,333
Completely agree. I am trying to develop...
Completely agree. I am trying to develop something one my own with information that I ALREADY KNOW about certain genes, but anyway not sure I have the patience for it.
What do you think about...
|
|
Forum: Bioinformatics
04-25-2014, 02:46 PM
|
|
Replies: 14
Views: 2,333
Not reinvent... adjust... or mold to my...
Not reinvent... adjust... or mold to my expectations as they grow...
I guess I don't find anything special in normalization data with a fudge factors... I can do that upfront with my library size...
|
|
Forum: Bioinformatics
04-25-2014, 02:26 PM
|
|
Replies: 14
Views: 2,333
Sure I can get the ranks of the p-values by...
Sure I can get the ranks of the p-values by running a loop to for all the genes and adjust the pvalue by number of samples divided by the rank.
I guess maybe now that I know how it works I'm not...
|
|
Forum: Bioinformatics
04-25-2014, 02:15 PM
|
|
Replies: 14
Views: 2,333
|
|
Forum: Bioinformatics
04-25-2014, 09:53 AM
|
|
Replies: 14
Views: 2,333
It doesn't change the fact that Gene1 had more...
It doesn't change the fact that Gene1 had more counts for the mutant than the WT and Gene2 had more counts for mutant than the WT but after nornaliation Gene2 was flipped and Gene1 was not.
It...
|
|
Forum: Bioinformatics
04-25-2014, 08:15 AM
|
|
Replies: 14
Views: 2,333
If I do a log fold change with the normalized...
If I do a log fold change with the normalized values I get roughly the same log fold change with the same sign as what is being spat out in the end by DESeq in the final result. Those normalized...
|
|
Forum: Bioinformatics
04-24-2014, 07:03 PM
|
|
Replies: 14
Views: 2,333
Flipped Results
I have a total of twelve samples
3 replicates per condition
Mutant(3) and Wild-Type(3) in exponential
Mutant(3) and Wild-Type(3) in stationary
Before I submit the raw counts to DESeq2...
|
|
Forum: General
04-24-2014, 03:36 PM
|
|
Replies: 7
Views: 3,571
|
|
Forum: General
04-24-2014, 02:32 PM
|
|
Replies: 4
Views: 2,361
|
|
Forum: General
04-24-2014, 02:23 PM
|
|
Replies: 4
Views: 2,361
|
|
Forum: General
04-24-2014, 01:43 PM
|
|
Replies: 7
Views: 3,571
I guess my reasoning was this.
If I sequence...
I guess my reasoning was this.
If I sequence three replicates that will show the variability between the replicates
If I pool a bunch together to make three replicates that came from pools of...
|
|
Forum: General
04-24-2014, 01:36 PM
|
|
Replies: 4
Views: 2,361
How DESeq2 Handles counts
Hypothetically
If I have 24 samples and I submit them to a facility to run my RNA-seq then can this happen?
The technician puts in varying amount of prepped library into the lanes so how does...
|
|
Forum: General
04-24-2014, 01:33 PM
|
|
Replies: 5
Views: 2,945
|
