SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 12 of 12
Search took 0.00 seconds.
Search: Posts Made By: reprogrammer
Forum: Epigenetics 08-11-2019, 05:34 PM
Replies: 0
Views: 505
Posted By reprogrammer
RnBeads (2.2.0) error when I run example 2

I am going to run the example (2) on Linux server. After download completed, it showed me this error.

> rnb.run.example(2)


2019-08-12 09:10:14 1.6 STATUS STARTED Downloading and...
Forum: Epigenetics 08-08-2019, 11:02 PM
Replies: 0
Views: 409
Posted By reprogrammer
Downstream analysis of methylkit

I have finished my RRBS analysis with methylkit R package. It returns me plenty of results, such as methylation distribution, coverage, clustering, annotation in the genome, DMRs and differential...
Forum: Bioinformatics 06-21-2016, 11:14 AM
Replies: 3
Views: 1,200
Posted By reprogrammer
Thank you Ryan, May I ask how do you filter the...

Thank you Ryan, May I ask how do you filter the top ~0.1% of covered sites? Is it also done by BiSeq package?
Forum: Bioinformatics 06-21-2016, 01:50 AM
Replies: 3
Views: 1,200
Posted By reprogrammer
Some Covered CpG sites is extremely high for RRBS with BiSeq package

I am using BiSeq package following bismark tools for RRBS analysis. I termed Covfiles as a BSraw file to include all the used 20 samples, and below is what it returns when I call...
Forum: Bioinformatics 05-12-2016, 09:00 PM
Replies: 16
Views: 9,919
Posted By reprogrammer
Yes, I had the same problem and it was solved by...

Yes, I had the same problem and it was solved by changing the relative path to the absolute path.

Btw, I do not know how to use Terminal and Linux, I am using Rbowtie package with R studio.
Forum: Bioinformatics 03-14-2016, 07:49 AM
Replies: 4
Views: 2,146
Posted By reprogrammer
Thank you jazz710 for sharing. I am a rookie for...

Thank you jazz710 for sharing. I am a rookie for R coding and data analysis. I have a really naive question: How to import my RNA-Seq alignment files into R?

My workflow: I upload my raw RNA-Seq...
Forum: Sample Prep / Library Generation 03-14-2016, 07:31 AM
Replies: 6
Views: 2,006
Posted By reprogrammer
Hi jdk787, Thank you so much for your...

Hi jdk787,

Thank you so much for your suggestion. Finally I got the PCR product with your guidance.

First I changed the Taq enzyme to Cx Pfu, I believe this is the major mistake I made. At the...
Forum: Sample Prep / Library Generation 02-24-2016, 12:01 PM
Replies: 6
Views: 2,006
Posted By reprogrammer
I noticed that I made a conceptual mistake. What...

I noticed that I made a conceptual mistake. What I am doing is whole-genome DNA methylation but not RRBS since I am using sonication biorupter to fragment genomic DNA.
Forum: Sample Prep / Library Generation 02-22-2016, 10:07 AM
Replies: 6
Views: 2,006
Posted By reprogrammer
Hi jdk787, I summarized my protocol and put...

Hi jdk787,

I summarized my protocol and put it in the attachment. Would you help me take a look is there anything wrong, please?
Thank you so much.
Forum: Illumina/Solexa 02-10-2016, 02:18 PM
Replies: 4
Views: 2,088
Posted By reprogrammer
I don' t understand how do you use beads instead...

I don' t understand how do you use beads instead of gel selecting, do you mean to use beads to purify the selected gel fragment but not use the column in the kit?
Forum: Sample Prep / Library Generation 02-10-2016, 07:17 AM
Replies: 6
Views: 2,006
Posted By reprogrammer
Low DNA yield after adapter ligation

Hi guys,

I am generating RRBS library recently. In the whole process I use Beckman Ampure Xp beads to purify (cleanup and elute) DNA. But only the step of adapter ligation showed a extremely low...
Forum: Illumina/Solexa 02-09-2016, 07:48 PM
Replies: 4
Views: 2,088
Posted By reprogrammer
I meet the same issue, have you figured out how...

I meet the same issue, have you figured out how to solve it, please?
Showing results 1 to 12 of 12

 


All times are GMT -8. The time now is 03:48 PM.


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