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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How can I convert ecat(.v) file to nifti(.nii) file in python?

I want to convert ecat file to nifiti file or ecat file to dicom so I can change it to .nii later. I would like it in python if possible. Do you have any library suggestion? Thank you
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How can I export a pruned phylogenetic tree in nexus format in R?

I have a phylogenetic tree with a lot of different populations and I wanted to removes most of them and apply new names to the labels. I wrote this code: ...
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How can I convert my tree to the correct nexus format?

I would like to use the program BayesTraitV4. I have my phylogenetic tree in NEXUS format but the program does not accept it. I checked the example data and while they are also in NEXUS format, they ...
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Getting rid of duplicates in a dictionary

I have a tsv file that lists the reads and read lengths from a FASTA file but some reads are duplicated - that's just from the analysis I did previously - but I want to only take one instance of the ...
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Converting convert .svs files into .mrxs format

I wish to convert Aperio AFI microscope .svs files from a pathology lab microscope into 3DHistech .mrxs format. Lab ppl have some pipeline X and they asked me to look into the matter. I can read the ...
pinegulf's user avatar
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How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?

I encountered the dichotomy in the context of PDBx/mmcif files, say, 6OSQ: each chain has a _entity_poly.pdbx_seq_one_letter_code...
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Do proper .fcs flow-cytometry files specify the gating hierarchy, so one may calculate cell-counts without specifying it themselves?

Do proper .fcs flow-cytometry files already have the gating hierarchy, so one may calculate cell-counts without extra work? https://github.com/whitews/FlowKit/ ...
Coo's user avatar
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Sequence format: grouping sequences within a flat file

Is there a sequence format allowing multiple sequences to be grouped across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure. To ...
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Does standardised format to write nutrients of a product exist?

Almost every food product has nutritional values labelling. Is there a digital format, one that would be standardised for use in such a case? For example I want to create a QR code which is going to ...
Candid Moon _Max_'s user avatar
2 votes
1 answer
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Converting genetic matrix to STRUCTURE

I want to convert a genetic matrix (rows are samples, columns are alleles) into a STRUCTURE file (output .str) within R. Is there a preferred way to achieve this? I've found genind_to_structure in the ...
akoontz11's user avatar
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How to properly annotate sequence variants and errors in a GenBank file format and how to keep track of successive versions of a GenBank file

EDIT By thinking over the issue, I realized it was mixing two linked but separate questions: Q1. How to handle the situation when there are divergences between a GenBank file and an actual or ...
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Is it valid VCF not to 'squash' positions with more than one ALT allele?

I'm seeing output from PBWT that looks like this: ...
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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
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1 answer
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How to extract a subset of individuals from a .bgen file?

I have 10,000 controls and 3000 cases and the .bgen file has genotype of 200,000 individuals. I would like to extract only those individuals from the .bgen file that are either cases or controls using ...
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pysam "Exec format" error

I am a beginner and trying to read a bam file in Python. The lines below throw the error ...
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Why do SAM and BAM use different coordinate systems?

BAM files are, at least as far as I know, simply binary compressed versions of SAM files. They have the exact same information and are used in the same way. Why then does the SAM format use a 1-based ...
terdon's user avatar
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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
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Which format is the most raw format

I wanted information regarding which format is considered the most raw from an illumina sequencer ? fasta fastq bcl bam As per my research it should be bcl but I am not sure.
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Not Able to pull genes due to file.fa error

I've recently been pulling TLR genes for different species and keep running across an error called file.fa whenever I start pulling them. Whenever I pull the first gene it's fine and makes the file.fa ...
dominic chang's user avatar
2 votes
2 answers
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Obtaining Whole Genetic Sequence

As an end-user of my own data, specifically raw DNA sequence (WGS, whole genome sequencing). How or where do one obtain such DNA data so that a biology hobbyist can perform bioinformatics on this? ...
John Greene's user avatar
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1 answer
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blast p-error with making directory

I tried running this command python blastp.py CmydPro tlr TLR.txt to extract the query sequence for the target species I'm looking at. However, whenever I try ...
dominic chang's user avatar
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1 answer
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Metagenome simulation from a concatenated FASTA file

I am trying to simulate metagenome sequencing. So I will start with a file with a lot of concatenated genomes. From there, I would like to randomly extract 10,000 sequences of length 200bps. I got ...
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Creating a tab delimited column [closed]

I have a blast file produced. I executed a blast(x) command outputting both "qeseqid" and ...
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1 vote
1 answer
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Is there a simple command for outputting a tab delimited columns?

I am working on a fasta file and am writing my command in nano within command-line and executing using python, also within a command line. My objective is to get my command to provide me with a tab ...
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creating a tab delimited file

I am working on a project using a fasta file. I am writing my command in nano within command-line and executing using python, also within my command-line. I would like my command to provide me with a ...
Edwardo's user avatar
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How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs?

I am having trouble with some underlying questions about my project. I have ran a Trinity tool to create a trinity.fasta file. To determine some underlying questions, I used the utility asm_stats to ...
AlphaQueUp's user avatar
6 votes
2 answers
220 views

BinaryCIF vs MMTF formats, which one to choose?

Both file formats are advertised as more memory/parsing efficent than old PDB format and its successor mmCIF format, but I can't understand the context (I'm a developer, but pretty new to the field of ...
ashas's user avatar
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1 answer
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What should be the numbers in the fastSTRUCTURE file?

The structure file for fastSTRUCTURE seem to be a table with rows and columns but the cells are all numbers, while my genotypes are simply bases. How could I know what I should insert there?
hiddenhospitalresearch's user avatar
8 votes
2 answers
6k 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
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2 votes
3 answers
1k views

Get start and end coordinates per chromosome

I will use GATK for SNP calling (HaplotypeCaller). I need to feed the interval file in the command, otherwise I get errors (even though I want to use the whole genome, not a subset - btw it's not the ...
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Wrong format .ped in PLINK

I know that I don't have the correct format in my .ped file for PLINK but I don't know how to convert it. My actual file is something like: ...
aguillenea's user avatar
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1 answer
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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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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
53 views

Parsing MSigDB Supplementary Collections

MSigDB recently added Supplementary Collections. The formatting is similar to the original MSigDB gene sets, but there is an additional metadata.txt file (link). ...
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1 answer
131 views

What type of information does an .sf file contain?

What is an .sf file. What information does it contain?
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Convert PAF format to SAM/BAM format

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use ...
Paul Endymion's user avatar
1 vote
1 answer
106 views

swap genotypes for specific fields of a vcf file

Is there a tool already established to "swap" the ref/alt information in the GT, AD and PL ...
aechchiki's user avatar
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6 votes
1 answer
75 views

Determine reference for reference-compressed SRA file

Note: this question was also asked on Github. I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an ...
Daniel Standage's user avatar
1 vote
4 answers
1k views

Index VCF file for rapid access by rsID?

With tabix one can index a VCF file for rapid variant retrieval based on genomic position. I'm wondering if there are any tools that will index a VCF file to allow rapid retrieval using rsIDs and/or ...
Daniel Standage's user avatar
3 votes
1 answer
93 views

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there ...
Guy Coder's user avatar
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1 answer
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Filter VCF for "CAF=[0.9,0.1]"

Related to this other question but in this case the CAF is defined as "An ordered, comma delimited list of allele frequencies...". I tried using vcffilterjdk and the command suggested by Pierre <...
Dario R's user avatar
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3 answers
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I have 23andme text files and would like to convert to SAM/BAM format

I would like to convert 23andme text file to NextGen to BAM file for Yfull.com to read. It is difficult to get answers on how to convert to SAM/BAM file for the 23andme text file to be converted to ...
Owance Jackie's user avatar
2 votes
1 answer
206 views

UniProt flat file. Interpreting format of SUBCELLULAR LOCATION. What does flag mean?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the section SUBCELLULAR LOCATION ...
Guy Coder's user avatar
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3 votes
4 answers
7k views

Can a gff file be converted to a fasta file?

I downloaded an annotated genome file in gff format here. I would like to use it for proteomics. Though I need it in fasta format. Is there any tool that converts gff to annotated fasta? I see the ...
Soerendip's user avatar
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2 votes
1 answer
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What is the "primer masterfile" format?

I am working with an amplicon kit from Swift Bioscience and they provide the primer locations in what they call a "masterfile". The format is like this: ...
terdon's user avatar
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1 vote
3 answers
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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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4 votes
3 answers
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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
1 answer
285 views

Plotting Ramachandran Plot from more than one PDB file

I want to plot a Ramachandran Plot for around 5000 PDB files in python that is saved in a folder in my system. I am searching for a way to make it without accessing each file by hard-coding each file ...
Sabyasachi Mishra's user avatar
6 votes
2 answers
395 views

Meaning of the FORMAT fields of the VCF file coming from GIAB project

After reading the GIAB paper in https://www.biorxiv.org/content/early/2018/05/25/281006 and its Figure 1, I am still having trouble understanding the data inside the GIAB VCF file for HG001 (...
Javier's user avatar
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2 votes
2 answers
571 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: ...
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