SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 308
Search took 0.02 seconds.
Search: Posts Made By: ETHANol
Forum: Illumina/Solexa 04-26-2015, 06:47 PM
Replies: 6
Views: 1,640
Posted By ETHANol
As mentioned with the new base caller you cannot...

As mentioned with the new base caller you cannot even specify a control lane if you want to. We do a lot runs that are only whole genome bisulfite sequencing so we use to have to do a control lane,...
Forum: Bioinformatics 06-18-2014, 09:12 PM
Replies: 0
Views: 1,377
Posted By ETHANol
multiple multiWig files for UCSC

There are some good examples on how to make a single multiWig file for visualization with a UCSC track hub, but I have 48 multiWig's I would like to make (i.e. 48 tracks from 288 wig files). Does...
Forum: RNA Sequencing 02-17-2014, 04:41 PM
Replies: 0
Views: 1,187
Posted By ETHANol
Multi-mapped reads - Lior Pachter

I was watching this video of Lior Pachter at CSHL last year and he's talking about what to do with multi-mapped reads and it makes no sense to me. What I think he is saying is that by assigning...
Forum: Illumina/Solexa 09-08-2013, 07:04 PM
Replies: 1
Views: 2,963
Posted By ETHANol
Off-line Basecaller (OLB) not demultiplexing

We (I) screwed up and lost the control lane from a run. The other lanes are methylC-seq libraries so they cannot be used for the control lane so we wanted to run Illumina's Off-line Basecaller (OLB)...
Forum: Illumina/Solexa 06-21-2013, 02:00 AM
Replies: 75
Views: 31,243
Posted By ETHANol
Just a word from a current observation is that if...

Just a word from a current observation is that if I measure the same libraries, which are only about 15 nM, on different days with Qubit HS DNA kit the concentration vary by up to 50%. The relative...
Forum: Sample Prep / Library Generation 06-07-2013, 03:29 AM
Replies: 2
Views: 1,413
Posted By ETHANol
SPRI beads (AMPure) work on any nucleic acid,...

SPRI beads (AMPure) work on any nucleic acid, dsDNA, ssDNA, RNA, DNA/RNA hybrid. The higher the PEG/NaCl concentration the smaller the fragments you recover, albeit the secondary structure of single...
Forum: Sample Prep / Library Generation 06-04-2013, 04:27 PM
Replies: 35
Views: 20,459
Posted By ETHANol
The original dUTP protocol required massive...

The original dUTP protocol required massive amounts of starting material because the ActD. If you removed ActD from the protocol you still got pretty good strandedness but required a lot less...
Forum: Sample Prep / Library Generation 05-30-2013, 12:22 AM
Replies: 35
Views: 20,459
Posted By ETHANol
Not sure what that means so.... From the...

Not sure what that means so....

From the Illumina website.
/truseq_stranded_mrna_lt_sample_prep_kit/questions.ilmn

How is strandedness maintained after DNA amplification?
Strandedness is...
Forum: Epigenetics 05-26-2013, 11:39 PM
Replies: 57
Views: 34,999
Posted By ETHANol
Wordpress.com has some problems. If you just...

Wordpress.com has some problems. If you just keep clicking reload a bunch of times it will eventually load. Annoying and I'd like to move my blog somewhere more reliable but it never makes it up to...
Forum: Illumina/Solexa 11-26-2012, 05:05 AM
Replies: 2
Views: 2,304
Posted By ETHANol
This is not your problem. It's something more...

This is not your problem. It's something more serious but you should use the KAPA HF polymerase. It is way better with GC-rich templates then the TruSeq polymerase and way better in general.

As...
Forum: Bioinformatics 11-09-2012, 07:18 PM
Replies: 9
Views: 6,772
Posted By ETHANol
HTSeq-count does the job. I have some scripts...

HTSeq-count does the job. I have some scripts that will take the grunt work out of it, but it takes a little time to set up and there's a reasonable chance it won't work on your platform....
Forum: Sample Prep / Library Generation 10-29-2012, 09:53 PM
Replies: 9
Views: 4,800
Posted By ETHANol
If you are doing acoustic shearing you can get...

If you are doing acoustic shearing you can get away with skipping the gel extraction and use AMPure to get rid of adapter-dimer. If you are using mononucleosomal DNA, in my experience you should do,...
Forum: Bioinformatics 10-17-2012, 05:46 PM
Replies: 9
Views: 6,772
Posted By ETHANol
The raw data (counts, i.e. DESeq, edgeR, etc) is...

The raw data (counts, i.e. DESeq, edgeR, etc) is the way to go for differential expression.

FPKM is the way to go for relative expression within a condition.

You just need to understand the...
Forum: Sample Prep / Library Generation 10-17-2012, 03:31 PM
Replies: 14
Views: 10,301
Posted By ETHANol
What are the size markers. Is the band in lane 1...

What are the size markers. Is the band in lane 1 about 120 bp. If so it is adapter dimer? Which would lead to the question of why the samples in lanes 2,3 and 4 are so small.
Forum: RNA Sequencing 10-16-2012, 04:26 AM
Replies: 7
Views: 4,099
Posted By ETHANol
I've left human total RNA purified with RNease on...

I've left human total RNA purified with RNease on my bench for a few days and run it on the Bioanalyzer and there was no detectable degradation (no it wasn't on purpose). But it might depend on...
Forum: Bioinformatics 09-22-2012, 07:07 PM
Replies: 23
Views: 31,974
Posted By ETHANol
In regards to qPCR validation, if you are using...

In regards to qPCR validation, if you are using the same RNA as you did your RNA-seq with, it is meaningless. Well, not meaningless, it means you have controlled for technical noise but not...
Forum: RNA Sequencing 09-13-2012, 10:11 PM
Replies: 5
Views: 1,591
Posted By ETHANol
See bedtools. Is your data RNA-seq data? If so...

See bedtools. Is your data RNA-seq data? If so you have to bed12 format to accommodate for gaps.
Forum: Epigenetics 09-10-2012, 01:03 AM
Replies: 6
Views: 4,018
Posted By ETHANol
I'll be the third to basically say the same...

I'll be the third to basically say the same thing. In my experience MeDIP-seq data is really messy and can be a bit hard to interpret. Not impossible but the data analysis probably going to be...
Forum: Bioinformatics 09-02-2012, 03:01 AM
Replies: 11
Views: 2,292
Posted By ETHANol
You'll never be able tell which gene are truly...

You'll never be able tell which gene are truly not expressed. That's how science works. We can only see what is, you can never see what isn't!!!!!

In this case you will always be able to say, if...
Forum: Bioinformatics 09-02-2012, 02:57 AM
Replies: 9
Views: 2,219
Posted By ETHANol
dpryan, thanks!!! but in that I don't know any C...

dpryan, thanks!!! but in that I don't know any C at all, I don't think I could work it into my data analysis pipeline.
Forum: Bioinformatics 09-01-2012, 06:26 AM
Replies: 1
Views: 3,398
Posted By ETHANol
How to get transcription factors from gene list

I have a list of human genes. I would like to know which one encode transcription factors. What would be the best way to do this?

Thanks in advance!!
Forum: Bioinformatics 08-31-2012, 05:31 AM
Replies: 9
Views: 2,219
Posted By ETHANol
Or you could run this R script to merge your...

Or you could run this R script to merge your HTSeq-count output files. Probably a little quicker then Excel if you have a lot of files. Anybody know how to do this with a BASH script??
...
Forum: Epigenetics 08-09-2012, 11:47 PM
Replies: 2
Views: 5,123
Posted By ETHANol
The links seem to be fine. Are you still having...

The links seem to be fine. Are you still having this problem? Send me a PM if you like.
Forum: Epigenetics 08-05-2012, 12:55 AM
Replies: 57
Views: 34,999
Posted By ETHANol
I've gone with as little as 2 ng and it worked...

I've gone with as little as 2 ng and it worked out o.k. I can't remember the exact number of cycles though.
Forum: RNA Sequencing 07-11-2012, 12:00 PM
Replies: 21
Views: 10,205
Posted By ETHANol
Iahoman -- probably because your libraries are...

Iahoman -- probably because your libraries are over amplified. There are a few threads on this topic here. Do a search. I do this to get the number of cycles right:...
Showing results 1 to 25 of 308

 


All times are GMT -8. The time now is 02:37 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO