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Recent Replies
Comment: How To Download .Gbk Files From Ncbi Website
by
Ram
34k
Hi, why did you delete this post, especially after it was replied to?
Comment: Trinity Statistic
by
GenoMax
106k
You will need to provide full path to where it is in your command e.g. `perl /path_to/TrinityStats.pl ....`
Comment: How to download BLAST+ on Centos
by
GenoMax
106k
Technically no installation should be needed.
- Download the executable here ([LINK][1]).
- Uncompress `tar -zxvf ncbi-blast-2.12.0+-x6…
Answer: How to transform a whole-genome callset into whole-exome callset?
by
h.mon
33k
There is no universal, consensus whole-exome annotation. There are, however, various platforms and versions of whole-exome library kits, wi…
Answer: Understanding the output of Negative Binomial in DESeq2
by
i.sudbery
13k
> Are zero is a default option of log2fold change to be considered as up and down?
Yes, by default, the null hypothesis is that the log2…
Comment: Homer finds same peak multiple times
by
ATpoint
53k
> I am using Homer to identify peaks in RNA-seq data
I know what ChIP-seq does and how it is analysed, but ChIP-seq discovers de novo wher…
Answer: A guide to modern genome assembly
by
Michael Dondrup
49k
There are some guidelines from the Earth BioGenome Project here: https://www.earthbiogenome.org/assembly-standards
These address quality r…
Comment: Understanding the output of Negative Binomial in DESeq2
by
swbarnes2
11k
You should look carefully at the values for those genes with extremely high log fold changes; if it's caused by most samples having zero ex…
Comment: Homer finds same peak multiple times
by
williamtmills
▴
10
It is somewhat custom, but peak calling is rather standard for sequencing data like CHIP-seq: [http://homer.ucsd.edu/homer/ngs/peaks.html][…
Comment: Homer finds same peak multiple times
by
ATpoint
53k
What is the `definition` of a peak in your context (how did you define it/produce it)?
RNA-seq produces no peaks, it produces counts per e…
Answer: Understanding the output of Negative Binomial in DESeq2
by
ATpoint
53k
> I have the attached the output of the model after fitting through DESeq2. In my output, there were five genes are upregulated and 2 genes…
Comment: A guide to modern genome assembly
by
Michael Dondrup
49k
Maybe this could become a part of the of the Biostars Handbook?
Comment: Homer finds same peak multiple times
by
williamtmills
▴
10
Chromosome #, start position, stop position.
Columns 2, 3, and 4.
Column 1 is an ID assigned to each peak.
Answer: How to download BLAST+ on Centos
by
Michael Dondrup
49k
I don't know which version of Centos you have, but try with Bioconda. Unless your Centos is extremely outdated, it should be the easiest wa…
Comment: How To Download .Gbk Files From Ncbi Website
by
GenoMax
106k
> NCBI seems to only be providing me with GenBank flat format files not
> regular gb/gbk
What does that mean? A GenBank format file will c…
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