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Forum: Oxford Nanopore 02-13-2019, 04:43 PM
Replies: 2
Views: 1,317
Posted By SuzuBell
Using Basic MinION Starter Pack in remote area for soil samples

I am not experienced with metagenomics/metatranscriptomics/soil microbiology/Nanopore technology, so please forgive if this post is misguided :)

I plan to conduct field work in a (slightly) remote...
Forum: General 10-23-2018, 04:18 PM
Replies: 1
Views: 1,392
Posted By SuzuBell
Align unmapped reads to virus genomes

Hello,

I am trying to determine how much of the unmapped reads from a transcriptome study align to viruses. My procedure so far has been to:

1) Download the complete genome of a virus in FASTA...
Forum: Sample Prep / Library Generation 06-18-2018, 01:44 PM
Replies: 0
Views: 807
Posted By SuzuBell
Maximize RNA obtained from clean environments

I am hoping to collect samples in environments that have very little nutrients (such as a clean room in a hospital). The amount of DNA that is collected from these environments tends to be pretty...
Forum: Sample Prep / Library Generation 06-18-2018, 01:31 PM
Replies: 1
Views: 874
Posted By SuzuBell
RNA-seq analysis from low biomass samples

I have access to a sample that we hope to run a microbial ecological study on. The problem is that each sample only has about one picogram of DNA.

What are the best molecular biology and/or...
Forum: Bioinformatics 05-24-2018, 12:52 PM
Replies: 1
Views: 862
Posted By SuzuBell
Determine mapping percentage from .fastq file

Is it possible to obtain the mapping percent from .fastq file?

If I do the following:

grep "@HISEQ" -c file.fastq

I believe I obtain the number of sequences. Can this be used to determine...
Forum: Bioinformatics 10-21-2017, 04:39 AM
Replies: 5
Views: 1,575
Posted By SuzuBell
Thanks GenoMax. 1) I agree it might be hard...

Thanks GenoMax.

1) I agree it might be hard to find a high false-positive rate example on its own. However, if that is the case, I am hoping to find an easily-reproducible example of a dataset...
Forum: Bioinformatics 10-20-2017, 05:10 AM
Replies: 5
Views: 1,575
Posted By SuzuBell
Thank you, I am trying to use real (not...

Thank you, I am trying to use real (not simulated) RNA-seq data.
Forum: Bioinformatics 10-19-2017, 02:09 PM
Replies: 5
Views: 1,575
Posted By SuzuBell
Talking Example RNA-seq datasets with low and high false-positive rates

Hello,

I am trying to obtain two example RNA-seq datasets. One has verified low false positive rate, and the other has verified high false positive rate.

Specifically, I am hoping to obtain 3...
Forum: General 07-06-2017, 06:57 PM
Replies: 0
Views: 1,448
Posted By SuzuBell
Examining possible extraneous variables in RNA-sequencing data

I have an RNA-sequencing dataset with 48 samples. I have a list of several possible extraneous variable values for each of the 48 samples. Some of these extraneous variables are categorical (lane1...
Forum: General 10-31-2016, 06:08 PM
Replies: 0
Views: 1,988
Posted By SuzuBell
argument "dispersion" is missing, with no default

Hi!

I am trying to perform DEG analysis on two treatment groups using edgeR. I originally planned to keep the analysis similar to what was used for another purpose previously. To prepare the data,...
Forum: General 10-17-2016, 06:07 PM
Replies: 1
Views: 2,226
Posted By SuzuBell
no slot of name "elementMetadata" for this object of class "SummarizedExperiment"

I have a count table that was saved as an .rda file. I was always able to open the .rda file in R simply using load("myData.rda"). Recently, upon trying to open the same file, I received an error in...
Forum: RNA Sequencing 10-17-2014, 09:03 AM
Replies: 1
Views: 1,101
Posted By SuzuBell
Maternal vs Zygotic gene expression

Are there any studies demonstrating evidence of zygotic mRNA showing greater gene expression than maternal mRNA (after "maternal to zygotic transition") that could affect results from RNA-seq...
Forum: Bioinformatics 04-27-2014, 06:38 PM
Replies: 5
Views: 1,504
Posted By SuzuBell
GenoMax, thanks for your help. The first...

GenoMax, thanks for your help.

The first download has crashed twice, and I have tried to start downloading it, but it has an estimation of 2-3 days for the past 2 hours.

However, the other two...
Forum: Bioinformatics 04-27-2014, 02:05 PM
Replies: 5
Views: 1,504
Posted By SuzuBell
Thanks again, dpryan. I think I may have...

Thanks again, dpryan.

I think I may have done it correctly then. I did download three items:

1) Homo_sapiens_UCSC_hg19.tar.gz (thanks for your explanation of this file)
2) UCSC compressed...
Forum: Bioinformatics 04-27-2014, 01:48 PM
Replies: 6
Views: 1,522
Posted By SuzuBell
dpryan, many thanks for your reply. I think...

dpryan, many thanks for your reply.

I think the fastq files are not compressed, because there is no extension. They are just named SRRXXXX.fastq. So, hopefully the BAM files will be smaller. Is...
Forum: Bioinformatics 04-27-2014, 11:35 AM
Replies: 5
Views: 1,504
Posted By SuzuBell
DESeq - need FASTA and GTF from same resource

I am following the DESeq protocol.

It suggests for me to download a reference genome sequence for the organism under study (homo sapiens) in (compressed) FASTA format. It also asks for me to...
Forum: Bioinformatics 04-27-2014, 10:43 AM
Replies: 6
Views: 1,522
Posted By SuzuBell
Space problem too.

Thanks for the reply, blancha. I am looking into transferring it via the helpful steps you provided.

The other problem I am coming up with is that although the fastq-dump command works on my...
Forum: Bioinformatics 04-26-2014, 11:42 PM
Replies: 6
Views: 1,522
Posted By SuzuBell
Installing a command/program to a remote computer

I downloaded fastq-dump. While it does the job on my personal computer, it runs very slow.

I have access to a remote computer that can get the job done faster. However, upon logging in, I realized...
Forum: Bioinformatics 11-07-2013, 06:27 PM
Replies: 2
Views: 5,116
Posted By SuzuBell
Daniel: Thank you, I did try to do...

Daniel:

Thank you, I did try to do that(simply rearrange columns), but am still uncertain for how to create certain columns of the .bed file. I think I can create Columns 1 2, 3, 5, 6, 7, 8:...
Forum: Bioinformatics 11-07-2013, 12:25 PM
Replies: 2
Views: 5,116
Posted By SuzuBell
Convert .gff3 file to 12-column .bed file

Hello:

I would like to convert .gff3 file to 12-column .bed file, as in this link under "BED Format" (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

I have thusfar used Galaxy from Penn...
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