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MirianT_NCBI
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antonioggsousa
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Ben_Ensembl
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ATpoint
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jpuntomarcos
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Recent Replies
Answer: ExomeDepth installation error
by
jared.andrews07
★
14k
```
install.packages("BiocManager")
BiocManager::install(c("Biostrings", "IRanges", "Rsamtools", "GenomicRanges", "GenomicAlignments"))
…
Comment: bioinformatics problems solved by graphs data structure
by
Pierre Lindenbaum
153k
(we speak english here)
de-novo assembly algorithms use graph-based structures. See https://en.wikipedia.org/wiki/De_novo_sequence_assembl…
Comment: bioinformatics problems solved by graphs data structure
by
abdelmalek.benmeziane
•
0
Je n'ai pas compris
Comment: bioinformatics problems solved by graphs data structure
by
Pierre Lindenbaum
153k
de-novo assembly ?
Comment: TSS of protein coding genes
by
Ram
38k
This is uncomfortable territory for me - I'm a computer guy mostly. I think it's safe to say that each transcript has a TSS and the consens…
Answer: Reduce poly-N regions longer than 200bp back to 200bp in a reference genome FAST
by
Pierre Lindenbaum
153k
eg for chr22, using sed ,j replace 1000 N with a few N :
samtools faidx ref.fasta "chr22" |\
awk '/^>/ {printf("%s%s\t",(N>0?…
Comment: how to get to a VCF from bam files
by
Ram
38k
I agree with GenoMax - you were using array jobs and now you've taken 2 steps backward - a series of jobs submitted using a shell loop is t…
Answer: PCA in gene expression
by
i.sudbery
16k
No, you should definitely not remove samples from a PCA on the basis that they are not separable between conditions. To do so would artific…
Comment: PCA in gene expression
by
i.sudbery
16k
Can you upload a picture of the PCA biplot for the benefit of those that have not seen it.
Comment: What means this Error when running a script in python??
by
Antonia
•
0
Thank you Pierre! It wasn't clear for me at all lol Trully thank you
Answer: How to find promoter sequence of a gene?
by
sunyeping
▴
40
Thank you all for the help!
To do the ChIP-seq, how many cells are needed? I am working on antigen-specific T cells in tissues, usually,…
Comment: What means this Error when running a script in python??
by
Pierre Lindenbaum
153k
in "configs/config_main.yaml", line 29, column 1
could not find expected ':'
the message is quite clear to me : There is missing …
Answer: How to derive conditional maximum likelihood of the sum of independent negative
by
Dan
▴
90
I try to answer this question. Based on the Conditional Likelihood defined in https://rss.onlinelibrary.wiley.com/doi/epdf/10.1111/j.2517-6…
Answer: Informations for gene summary are missing in eutils api of NCBI?
by
MirianT_NCBI
▴
440
Hi,
You can use [NCBI Datasets][1] to retrieve gene information in JSON format. Using the gene id you used as an example, you can do thi…
Comment: How to find promoter sequence of a gene?
by
Trivas
▴
690
You can use the UCSC genome browser to get the the sequence of X bases upstream of a gene, then use tools in MEME-suite/JASPAR to look for …
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