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Search: Posts Made By: TheSeqGeek
Forum: Bioinformatics 02-19-2015, 06:07 AM
Replies: 8
Views: 1,719
Posted By TheSeqGeek
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
Posted By TheSeqGeek
So what's the tool?

So what's the tool?
Forum: Bioinformatics 02-13-2015, 12:57 PM
Replies: 8
Views: 1,719
Posted By TheSeqGeek
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
Posted By TheSeqGeek
I tried using excel and quickly realized I need...

I tried using excel and quickly realized I need to run loops.
Forum: Bioinformatics 02-10-2015, 12:11 PM
Replies: 8
Views: 1,719
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
In bacteria I don't think you can get away with...

In bacteria I don't think you can get away with those short times. Takes time to pass through all the barriers.

What was your final quench concentration for Tris?


Quote from a this...
Forum: Sample Prep / Library Generation 05-07-2014, 03:20 PM
Replies: 23
Views: 36,098
Posted By TheSeqGeek
I'm a bit late to the party but what are those...

I'm a bit late to the party but what are those gels showing exactly... The Tris looks the same in both conditions...

I am doing ChiP-seq now myself
Forum: Bioinformatics 04-27-2014, 12:57 PM
Replies: 6
Views: 3,593
Posted By TheSeqGeek
solved!! needed to make the fasta file into...

solved!!

needed to make the fasta file into a single line

perlscrip called singleline.pl


#!/usr/bin/perl -w
#perl fa2oneline.pl sample.fa > out.fa
# downloaded from...
Forum: Bioinformatics 04-27-2014, 12:39 PM
Replies: 6
Views: 3,593
Posted By TheSeqGeek
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
Posted By TheSeqGeek
Neat thanks! schöne Wochenende

Neat thanks!

schöne Wochenende
Forum: Bioinformatics 04-25-2014, 02:55 PM
Replies: 14
Views: 2,333
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
I used a Bonferroni adjustment. The most...

I used a Bonferroni adjustment. The most stringent one as I understand it to be.
Forum: Bioinformatics 04-25-2014, 09:53 AM
Replies: 14
Views: 2,333
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
that's true and I agree completely... If this was...

that's true and I agree completely... If this was a free experiment I would have run 100 samples per condition :)
Forum: General 04-24-2014, 02:32 PM
Replies: 4
Views: 2,361
Posted By TheSeqGeek
excellent thank you size factors are around...

excellent thank you

size factors are around 0.9 - 1.1 bla bla bla
Forum: General 04-24-2014, 02:23 PM
Replies: 4
Views: 2,361
Posted By TheSeqGeek
thanks you have been a great PI in my research so...

thanks you have been a great PI in my research so far :)


quick code in R for size factors?
Forum: General 04-24-2014, 01:43 PM
Replies: 7
Views: 3,571
Posted By TheSeqGeek
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
Posted By TheSeqGeek
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
Posted By TheSeqGeek
Thank you.... I looked on Wikipedia and didn't...

Thank you.... I looked on Wikipedia and didn't know which one of those... PMF will do

Thanks
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