Questions tagged [conversion]

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Generate simulated bam for certain snps

I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
Shafayet Rahat's user avatar
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1 answer

convert GT:PL format to GT:GP format

I have a vcf info formatted in GT:PL. ...
Shafayet Rahat's user avatar
2 votes
1 answer

need bam file for pilon

I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file. How do I make a BAM file of the resulting assembled.fasta?
rimo's user avatar
  • 923
1 vote
1 answer

How to convert amino acid sequence to SMILES format

I have an amino acids string "MKGK" and I would like to convert it into SMILES format. I tried two approaches. First with PepSMI which gives me: ...
littleworth's user avatar
3 votes
1 answer

converting mouse genes to human genes

I'm trying to convert mouse genes from PTX data to human genes in order to do a comparison with patient data to see what genes are being conserved. I'm using this file for the orthologs. http://www....
mmpp's user avatar
  • 371
1 vote
2 answers

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
0 votes
1 answer

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
1 vote
3 answers

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from I opened the "c5.all.v6.2.symbols.gmt" file in csv format and It looks like below: I want to ...
beginner's user avatar
  • 631
8 votes
2 answers

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart. I tried to get a kind of conversion table for all human genes. ...
floatingpurr's user avatar
4 votes
1 answer

Missing data mappings in while trying to convert Genes Ensembl Ids to Entrez Ids

I need to convert a lot of Ensembl Ids to the relative counterpart in Entrez (e.g., ENSG00000157764 > 673). I found ...
floatingpurr's user avatar
4 votes
2 answers

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
  • 612
6 votes
1 answer

Entrez or Ensembl gene IDs?

I'm using several datasets that are encoded using either Entrez or Ensembl IDs to specify genes, and need to decide on which to standardise on. Are there any major reasons to use one over the other? ...
user avatar
13 votes
6 answers

Converting gene names from one public database format to another

This is a question from /u/apivan19 on reddit. The original post can be found here. I have some proteomics data that was given to me with the UniProt gene identifiers in column 1. I've been trying to ...
gringer's user avatar
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