Questions tagged [identifiers]

Use this tag if your question is about translating some identifiers to others or about the rules of certain identifiers.

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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 ...
Dandelion's user avatar
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2 votes
1 answer
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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 ...
user27815's user avatar
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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 ...
Riesz98's user avatar
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2 answers
267 views

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 ...
medicalresearcher's user avatar
2 votes
1 answer
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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: ...
Marco's user avatar
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1 answer
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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 ...
bmv's user avatar
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3 votes
3 answers
950 views

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 ...
Cornelius Roemer's user avatar
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2 answers
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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 ...
Fernando D'Andrea's user avatar
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2 answers
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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....
Kishor Kumar Sarker's user avatar
1 vote
1 answer
1k views

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 ...
user345394's user avatar
1 vote
2 answers
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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 ...
user345394's user avatar
1 vote
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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 ...
ecprimate's user avatar
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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 ...
Spartan 117's user avatar
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1 answer
1k views

Mapping UniProt id to Entrez id

How can we get mapping from UniProt id to Entrez ID? I have UniProt id, but want to convert those ids to Entrez or Ensembl id.
user224050's user avatar
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Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?

I have a nucleotide sequence where I am interested in aligning reads distinctly to one or another portion of the sequence. However, I would like to use a visualization tool such as IGV to view these ...
Dan's user avatar
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Why the gene symbol aliases have significantly different sequences?

"Aliases" or "Synonyms" should represent the same gene but with different names. But when I try to find the sequence of one alias and try to match with another alias they are ...
Riq's user avatar
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how to get FlyBase ID conversion table

FlyBase uses systematic naming of genes, transcripts and proteins in a format FBtypeNUMBER. However, the numbers are not the same for genes and their products. For ...
Kamil S Jaron's user avatar
2 votes
2 answers
218 views

What do these files / annotations mean?

I have no experience in Bioinformatics and I need to understand what the annotations given here mean (I am including the first few lines, please see the link for more): ...
Dendrobium's user avatar
1 vote
1 answer
377 views

Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number

I annotated my bacterial genomes using the new NCBI Prokaryotic Genome Annotation Pipeline and now, I want to annotate EC-numbers. In the master annotation file (.gff), I get the RefSeq-ID of every ...
MrTomRod's user avatar
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7 votes
1 answer
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Gene not found in Affymetrix expression profiles

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249. I downloaded the following file in ...
wrong_path's user avatar
1 vote
1 answer
41 views

Does read sequence identifier need to be unique for proper alignment?

I am preprocessing a set of scTHSSeq reads in which each read sequence identifier has been replaced with the cell barcode, e.g.: ...
gc5's user avatar
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1 vote
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Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
dedek's user avatar
  • 111
1 vote
2 answers
203 views

Obtaining identifier from plot of sequence GC%

I was looking at this script from https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc297 and wanted to use it to determine outliers for tentative Horizontal gene transfer. The data set is ...
Ro Siv's user avatar
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3 votes
1 answer
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Folded Protein Chunk Dimensional Classification?

Are there known dimensional measurements for the classification of folded proteins given a starting chunk/domain as defined by something like the clustering functionality of MSM Builder? Examples of ...
CoryG's user avatar
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1 vote
1 answer
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What are the algorithms for biometric identification in large database?

I have been thinking about this problem and reading some related papers for sometime. The problem can be described as follows: Suppose that each biometric template is a $d-$dimensional vector. A ...
Paradox's user avatar
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5 votes
3 answers
719 views

How to determine the primary Uniprot accession number from a set of accession numbers?

Given a list of Uniprot IDs that are linked to an Ensembl gene ID, is there a way to systematically determine the UniProt accession corresponding to the protein product of the gene's primary ...
James Draper's user avatar
4 votes
1 answer
489 views

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...
terdon's user avatar
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3 votes
1 answer
128 views

What database do gene IDs starting with sp_v2 refer to?

I am a student trying to analyze GEO2r datas for one of my courses. The IDs given in the output are different for different series. I need to convert all of them to a similar format. In this process ...
hhoomn's user avatar
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5 votes
2 answers
1k views

Fasta Sequence Identifier format?

I have been analyzing some virus DNA from the NCBI databases. The fasta sequences that I recieve from them have header lines that look like this: ...
Jon Deaton's user avatar
4 votes
2 answers
319 views

Convert Reactome Protein IDs to Pathway IDs?

I have a list of about 50k 'Protein IDs' from Reactome. Is there a simple way to get all the corresponding 'Pathway IDs' for each protein? What is the best service to use? (I'm guessing I can use the ...
Dan's user avatar
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11 votes
1 answer
947 views

How to read and interpret a gene expression quantification file?

I have a gene expression quantification file from TCGA that contains the following lines: ...
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