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 ...
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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/
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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 ...
M__♦
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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 ...
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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 ...
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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:
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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 ...
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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:
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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 ...
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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?
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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 ...
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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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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 ...
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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 ...
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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 ...
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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?
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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 ...
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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:
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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 ...
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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):
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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
<...
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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 ...
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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 ...
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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 ...
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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:
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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 ...
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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?
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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 ...
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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 (...
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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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