Forum: Oxford Nanopore
10-07-2020, 04:40 AM
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Replies: 0
Views: 1,234
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Forum: RNA Sequencing
10-07-2020, 04:33 AM
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Replies: 2
Views: 3,329
Thank you for your response. I can certainly...
Thank you for your response. I can certainly write some scripts that use likelihood models to estimate which tissue each feature may be derived from.
As a confirmation, it seems there are no...
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Forum: RNA Sequencing
01-10-2020, 07:17 AM
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Replies: 2
Views: 3,329
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Forum: Oxford Nanopore
02-13-2019, 05:43 PM
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Replies: 2
Views: 4,244
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Forum: General
10-23-2018, 05:18 PM
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Replies: 1
Views: 2,005
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...
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Forum: Sample Prep / Library Generation
06-18-2018, 02:44 PM
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Replies: 0
Views: 978
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...
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Forum: Sample Prep / Library Generation
06-18-2018, 02:31 PM
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Replies: 1
Views: 1,054
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...
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Forum: Bioinformatics
05-24-2018, 01:52 PM
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Replies: 1
Views: 1,613
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...
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Forum: Bioinformatics
10-21-2017, 05:39 AM
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Replies: 5
Views: 2,043
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...
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Forum: Bioinformatics
10-20-2017, 06:10 AM
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Replies: 5
Views: 2,043
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Forum: Bioinformatics
10-19-2017, 03:09 PM
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Replies: 5
Views: 2,043
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Forum: General
07-06-2017, 07:57 PM
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Replies: 0
Views: 2,236
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Forum: General
10-31-2016, 07:08 PM
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Replies: 0
Views: 2,809
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,...
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Forum: General
10-17-2016, 07:07 PM
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Replies: 1
Views: 2,964
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Forum: RNA Sequencing
10-17-2014, 10:03 AM
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Replies: 1
Views: 1,331
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...
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Forum: Bioinformatics
04-27-2014, 07:38 PM
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Replies: 5
Views: 1,819
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...
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Forum: Bioinformatics
04-27-2014, 03:05 PM
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Replies: 5
Views: 1,819
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...
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Forum: Bioinformatics
04-27-2014, 02:48 PM
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Replies: 6
Views: 1,818
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...
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Forum: Bioinformatics
04-27-2014, 12:35 PM
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Replies: 5
Views: 1,819
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...
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Forum: Bioinformatics
04-27-2014, 11:43 AM
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Replies: 6
Views: 1,818
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...
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Forum: Bioinformatics
04-27-2014, 12:42 AM
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Replies: 6
Views: 1,818
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...
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Forum: Bioinformatics
11-07-2013, 07:27 PM
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Replies: 2
Views: 6,156
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:...
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Forum: Bioinformatics
11-07-2013, 01:25 PM
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Replies: 2
Views: 6,156
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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