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Recent Replies
Answer: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
by
Michael
•
0
I ran into this issue. It was caused by the FASTA data being included in the GFF3 file I was working with. I truncated the file starting a…
Comment: NCBI API, Perl
by
MirianT_NCBI
▴
590
Hi,
Following Genomax' suggestion, you can use NCBI Datasets. I used the IDs you posted to create a list.
```
LOC105370256
LOC105377806
LO…
Comment: How to quantification proteomics data
by
eqoa45
•
0
Hello, can I ask how did you manage the solution?
Comment: Perl. How to retrieve data until a keyword in GenBank?
by
Fungi-Beware!
▴
10
Doing it this way outputs the info, but it doesn't preserve the paragraphs (all the info gets smashed into a single line).
Is there a way …
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
by
Daniel
▴
30
I am referring to chr2.maf which I found here (last updated 2017): https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz30way/maf/
PHAST …
Answer: Spatial transcriptomics without the h5 file
by
Arvin
•
0
If you still have the problem,
I have stablished a code for you to read any spatial expression using gene expression and spatial coordinate…
Comment: Trying to edit VCF file
by
peavy
•
0
I'm aware. I manually typed each one but those 3 when I submitted. I actually made that mistake the first time around and only kept the 3 I…
Comment: Trying to edit VCF file
by
Pierre Lindenbaum
154k
option -S in bcftools view is for the samples you want to KEEP.
Comment: Get relationships and hierarchies for GO terms
by
Buffo
★
2.2k
Something like [GO enrichment analysis][1]?
[1]: http://geneontology.org/docs/go-enrichment-analysis/
Comment: NCBI API, Perl
by
GenoMax
129k
NCBI `datasets` does not seem to want to work with those ID's but that may be my limited knowledge. NCBI support staff visits Biostars and …
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
by
Maximilian Haeussler
★
1.5k
Can you provide an example? Which MAF file are you referring to, on the UCSC and Ensembl side. I can imagine a dozen different things that …
Comment: Trying to edit VCF file
by
peavy
•
0
Y Z and AA ideally wont be there or come up in the vcf file if I removed them proper so I'm wondering what the issue is in the initial code.
Comment: Trying to edit VCF file
by
Pierre Lindenbaum
154k
> I noticed that there was still columns for what I removed from the file.
so, what should we see in your image ??
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