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Search: Posts Made By: beki.renberg
Forum: General 01-26-2018, 09:54 AM
Replies: 6
Views: 3,217
Posted By beki.renberg
Question I need the same information

Have you been able to find any information on this? I am looking into the same issues. I have asked a few people who work in genomics cores and they all still use the Agilent Bioanalyzer. I need...
Forum: RNA Sequencing 11-24-2015, 09:32 AM
Replies: 7
Views: 2,050
Posted By beki.renberg
@ blancha - Thank you for the information and...

@ blancha - Thank you for the information and insight.
Forum: RNA Sequencing 11-23-2015, 10:09 AM
Replies: 7
Views: 2,050
Posted By beki.renberg
@GenoMaz - Yes, the ultimate aim is to compare...

@GenoMaz - Yes, the ultimate aim is to compare conditions A and B (and eventually C and D).

We did the comparisons between the biological replicates within condition A to just see how much...
Forum: RNA Sequencing 11-23-2015, 09:52 AM
Replies: 7
Views: 2,050
Posted By beki.renberg
Thank you for the feedback on many different...

Thank you for the feedback on many different things. I will look into doing a principal component analysis of the data to see how it clusters and will stop doing one-to-one comparisons of the...
Forum: RNA Sequencing 11-20-2015, 09:55 AM
Replies: 7
Views: 2,050
Posted By beki.renberg
Question Bacterial RNA-Seq Differential Gene Expression Biological Reps vs Exp Conditions

We have 6 bacterial samples that we are working with - 2 sets of 3 biological replicates (condition A -1, 2, 3 and condition B 1, 2, 3)- that we performed stranded RNA-Seq on. We are completely new...
Forum: General 11-05-2015, 04:07 AM
Replies: 10
Views: 1,557
Posted By beki.renberg
Thank you for the heads up about the zcat...

Thank you for the heads up about the zcat command.

Just to make sure, I should double check my concatenated files and make sure that all the the reads that I expect to be there, are actually...
Forum: General 11-03-2015, 10:46 AM
Replies: 10
Views: 1,557
Posted By beki.renberg
Follow-up. I ended up installing Oracle...

Follow-up.

I ended up installing Oracle VirtualBox (https://www.virtualbox.org/) and installing Ubuntu as a virtual machine so I could combine the fastq files using the zcat command in the...
Forum: General 11-02-2015, 08:56 AM
Replies: 10
Views: 1,557
Posted By beki.renberg
Thank you for the clarification and for the info...

Thank you for the clarification and for the info on BBMap. I will look into it.

I do have the option to run a virtual machine on this box and I have discussed it with my supervisor multiple times...
Forum: General 11-02-2015, 08:24 AM
Replies: 10
Views: 1,557
Posted By beki.renberg
For clarification, do you mean combining the four...

For clarification, do you mean combining the four lanes for R1 into one file and the four lanes for R2 into one file for a total of 2 files that are paired-end OR combining all 8 files (L1_R1, L1_R2,...
Forum: General 11-02-2015, 07:58 AM
Replies: 10
Views: 1,557
Posted By beki.renberg
Arrow RNAseq Pipeline questions

We recently ran our FIRST RNAseq run on our new Illumina NextSeq. We ran a paired-end run with 12 indexed samples. The data generated comes in 8 fastq files for each sample (4 lanes, Read 1, Read 2)...
Forum: Introductions 11-02-2015, 07:42 AM
Replies: 0
Views: 598
Posted By beki.renberg
Smile Introduction

Hello all. I recently finished my PhD in Biological Sciences and have transitioned a little into the world of bioinformatics. I was hired to join my group to get their NGS up and running and the...
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