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Recent Replies
Comment: How to extract sample id using bcftools or vcftools
by
Ömer An
▴
230
You can refer [here][1].
[1]: http://manpages.ubuntu.com/manpages/impish/man1/vcf-query.1.html
Answer: How to find the names of elements while parsing PDB files via biopython?
by
Tzunami
•
0
Found the solution (atom entries have an attribute called element which returns the element of the corresponding atom) -
for model …
Comment: plant viruses sequences
by
Ric
▴
350
Thank you, I click the Download bottom from your first link, selected land plants and downloaded the following files:
```
$ ls -hlatr
total…
Comment: plant viruses sequences
by
GenoMax
104k
[**Viral genomes browser**][1] is available from NCBI. Use `filter by host` (land plants seems to generate plenty of results). There is a `…
Comment: inquiry related to snpsift
by
Kevin Blighe
75k
As with many things in bioinformatics, the VCF specification has been misused over the years. Take into account, also, that different progr…
Comment: gene expression of specifics gene
by
Bioinformatics1
•
0
I have log2(Fold Change) for two groups. Is there any instruction/pipelines I can use for gene expression using log2(Fold Change) in R?
M…
Answer: use a list of id to extract sequence from different genomics
by
Pierre Lindenbaum
137k
[linearize][1] and extract the ID at the same time, sort both list, join, restore the fasta:
join -t $'\t' -1 1 -2 1 \
<…
Comment: What does betaPrior do in DESEQ?
by
i.sudbery
12k
Those DE genes - is that after a log fold change cut off?
Answer: How to filter VEP results of "missing values"
by
Yiming
▴
10
Thank you so much!
I found an error with my code. And this works:
filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf …
Comment: use a list of id to extract sequence from different genomics
by
GenoMax
104k
Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. <br />
<img src="…
Comment: gnomaAD exome and genome AF differences
by
humzakhan340
•
0
The point that genomes are much larger and more computationally intensive to work with is well-taken.
However, promoter information is not…
Comment: ERROR [mem_sam_pe] paired reads have different names -- during binning in metaW
by
swbarnes2
10k
Do you understand what the problem is? Have you figured out which step introduced it?
Comment: inquiry related to snpsift
by
rheab1230
•
0
I have one question related to earlier step where you are formating the .vcf file.
You are removing white space and removing format tags ex…
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