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Questions tagged [file-formats]

File format are sets of defined rules to organise a specific type of data. Common file format in bioinformatics include FASTA, FASTQ, SAM, BAM, VCF.

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18 votes
7 answers
16k views

How to convert FASTA to BED

I have a FASTA file: ...
SmallChess's user avatar
  • 2,699
41 votes
4 answers
61k views

What is the difference between FASTA, FASTQ, and SAM file formats?

I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another? Based on Wikipedia pages, I can't ...
kenorb's user avatar
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13 votes
6 answers
405 views

Are there any databases of templates for common bioinformatic file formats?

I want some templates of different file formats that I can use to test my scripts and identify possible bugs in my code. For example, consider nucleotide FASTA, a simple but often abused format, I ...
Chris_Rands's user avatar
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10 votes
4 answers
280 views

Annotation format design

Bashing file formats is a favorite pastime in bioinformatics, and annotation file formats such as GFF and BED seem to get special attention. A lot of this frustration stems from community's shockingly ...
Daniel Standage's user avatar
9 votes
5 answers
1k views

Converter between PDB or mmCIF and MMTF

I'd like to test MMTF, a new format for storing biomolecular structures which is promoted by RCSB as a more compact alternative to mmCIF and PDB. From MMTF FAQ: How do I convert a PDBx/mmCIF ...
marcin's user avatar
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8 votes
2 answers
7k views

How is the GT field in a VCF file defined?

As my question in SO was closed and asked to be posted in this forum, I am posting it here. I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain ...
The Great's user avatar
  • 227
4 votes
1 answer
3k views

How to quickly and robustly convert between mmCIF and PDB?

There is already a question on PDB/CIF to MMTF, however what is a robust way to programmatically go between PDB and CIF files? For example I can use a python script from this gist that relies on ...
James's user avatar
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4 votes
3 answers
6k views

How to convert Bed file to fasta file?

I have Bed file containing start and end of a sequence, and I need to convert it to fasta format, any recommendations?
Nour El-Islam Awad's user avatar
2 votes
2 answers
309 views

What is the file .mums created by mummer?

I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are: 1.create a file .mums with the following command line: ...
HelpNeederStudent's user avatar
2 votes
2 answers
587 views

How to filter for "CAF=0.5747,0.4253"

In my gzipped VCF file I have many variants, and they report allele frequency such as: ...
SmallChess's user avatar
  • 2,699
1 vote
3 answers
6k views

How to convert data in gmt format to dataframe?

I downloaded c5: gene ontology gene sets file from http://software.broadinstitute.org/gsea/downloads.jsp 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
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0 votes
1 answer
37 views

Is it valid VCF not to 'squash' positions with more than one ALT allele?

I'm seeing output from PBWT that looks like this: ...
Dan Bolser's user avatar
0 votes
1 answer
85 views

How to format my file using linux tools?

I have an imputed dosage for chr 22 file. its content is: ...
Rhea Bedi's user avatar