Questions tagged [identifiers]
Use this tag if your question is about translating some identifiers to others or about the rules of certain identifiers.
33
questions
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KEGG IDs and gene IDs going unrecognized in Cytoscape metscape software
I'm new to using metscape and am having some trouble with entering my compound IDs and gene IDs into the system. When I enter my compound IDs as KEGG IDs, around a quarter of my data goes unrecognized ...
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4
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2
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68
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Converting Gene Symbols to Entrez ID in ambiguous cases
Context: I am trying to perform GSEA GO analysis using data from the GeoMx Digital Spatial Profiler. The GeoMx DSP looks at the expression of a panel of mRNA transcripts using a set of detection ...
- 41
1
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83
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VEP annotation INFO field Ensembl IDs and locations
I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line).
However, my output is ...
- 383
2
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69
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Standardizing Variant IDs best practise
I'm currently pondering on the best approach to handle and standardize variant IDs within our department to mitigate the challenges associated with rsids and the potential ambiguity of just using ...
- 121
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37
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David tool online not converting most genes
I'm using DAVID tool online, in order to perform functional annotation chart. I extracted the most relevant genes from a dataset (GSE73304), but have the problem that DAVID is not able to understand ...
- 41
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2
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495
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Lifting snp rsid build 37 to 38
I’m looking to lift over a dataset of GWAS summary stats from build 37 to 38, including converting rsid. Downstream it is to be used for co-localisation with another dataset of build 38.
Would anyone ...
2
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1
answer
37
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Retrieval protein definition from accession ID
I have a list of protein accessions:
XP_025107904.1
PVD22034.1
AJA37836.1
How can I obtain the definition of the protein, and the related organism?
Output:
...
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71
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CLI access to genomes/proteomes by BioSample ID [duplicate]
This question was also asked on Biostars
I'd like to download multiple genome assemblies or proteomes using a set of BioSample IDs from NCBI.
I'm able to find the assemblies belonging to the BioSample ...
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3
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How to get strain names/ids contained in a multi FASTA file using seqkit?
FASTA files can be very big and unwieldy, especially if lines are at most 80 characters, one can't speed up browsing them by using less with ...
- 409
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2
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55
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BAM files with no RNAME and POS, how to map contents to SNPs?
I have a set of 4 .bam files containing the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with ...
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2
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48
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Remove variable sequence component within a tree text file
I have a gene tree file of 436 orthologue genes from 6 species. I want to remove unwanted extensions as it looks massy after visualization. My file looks like:
(TRINITY_Clupea_DN5452_c0_g1_i1.p1:0....
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Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids
I want to use a file available on a database called DepMap (https://depmap.org/portal/download/). This file called ...
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2
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What is the best way to programmatically convert Ensembl ids from one release to other? e.g. transcript ids from release 75 to 100
3 solutions that I had to unfortunately rule out.
Potential solution #1
As far as I know, the conventional way is to do this is by using CCDS ids (e.g. using biomart). However, the issue is that, as I ...
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992
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How to replace sequence identifiers in a fasta with OTU IDs from another file?
I'm pretty new to Unix and bioinformatics and having a hard time accomplishing the following. I have one FASTA file with sequences and headers, and one OTU ID mapping file (.txt) with OTU IDs and ...
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What type of Protein ID is this?
I got a FASTA file from NCBI RefSeq.
These proteins are annotated with IDs like this : protein_id=XP_019970915.1.
What type of ID is this? I would like to have them converted in TrEMBL IDs in order to ...
- 147