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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29 views

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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1answer
208 views

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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2answers
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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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1answer
33 views

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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1answer
71 views

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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1answer
66 views

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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1answer
46 views

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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2answers
72 views

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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1answer
165 views

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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2answers
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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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50 views

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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960 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 ...
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3answers
404 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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746 views

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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1answer
621 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 ...
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2answers
214 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): ...
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1answer
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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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1answer
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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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1answer
1k views

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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1answer
82 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 ...
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0answers
56 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 ...
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3answers
651 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 ...
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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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1answer
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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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3answers
511 views

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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1answer
164 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 ...
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4answers
4k 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 ...
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1answer
159 views

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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3answers
3k 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 ...
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3answers
3k 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?
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1answer
180 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 ...
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2answers
276 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 (...
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420 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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1answer
790 views

get gene lines from gtf file

I would like to retrieve gene lines from a GTF file for which I only have exons & transcripts lines (output from Cufflinks) and alternative splicing possible. I need gene lines for compatibility ...
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2answers
580 views

Script to run everything in a loop for extracting tar.gz files into fastq and to bam with alignment?

Original tar.gz files look like below: ...
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1answer
95 views

How to calculate call detection values in microarray datase if .cel file unavailable

I would like to do a differential gene expression analysis on a microarray data. From the literature, I understood, call detection (Present, Absent, Marginal) has to be done to minimize false ...
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68 views

Which data format for stranded coverage data

I need tools I am writing to output data in terms of score for each base in the genome. The format needs to be indexed for fast random access. The obvious choices are bigWig and tabix-index bedgraph ...
6
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1answer
253 views

Run gffread in multi-thread mode

Is there any possibility to run gffread in multi-thread mode? The answer seems to be 'no' from the manual (or gffread -h), as no multi-thread option is mentioned. ...
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2answers
314 views

seqret error when trying to transform GFF3 and FASTA files into EMBL format

I am using the tool seqret from emboss to transform an annotation file in GFF3 format and a FASTA file into an EMBL file because Wormbase does not supply an EMBL file with annotation and sequence ...
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1answer
348 views

Can a data file in VCF format be converted into FASTA?

I'm considering purchasing the 'MyGenome' product by Veritas Genetics to analyze my genome for a project. I'd like the data to be in FASTA format, but Veritas only provides VCF data. Is it possible to ...
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1answer
739 views

Why would someone use a CRAM instead of a BAM?

I had this question from a graduate student yesterday, and I was stuck. What should I say? Why use a CRAM instead of a BAM? When is it a good idea to use a CRAM instead of a BAM? When is it a bad ...
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1answer
383 views

What are the differences between BNGL (BioNetGen Language) and SBML (System Biology Markup Langague) formats?

Per request from meta comment. I am self-learning about whole cell modeling, specifically An introduction to whole-cell modeling and Fundamentals of Systems Biology: From Synthetic Circuits to Whole-...
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1answer
141 views

seqret: Warning: bad /protein_id value

I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence: ...
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1answer
275 views

Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?

On this Biopython tutorial, they describe how to import a multiple sequence alignment in the Mauve (XMFA: extensible multi fasta format). So I imported the AlignIO module: ...
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3answers
732 views

Infer missing UTR features in GFF3 file

I am working on a GFF file that is missing the 5'UTR and 3'UTR information. For example: ...
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3answers
416 views

How to indicate the END of a haplotype block in VCF?

In VCF I know how to indicate that two genotypes are in the same phase by using consecutive "0|1" and "1|0" genotype fields, for example. However, how do I deal with the case that the first two ...
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2answers
2k views

bcftools output vs. bgzip

I've got what seems like it should be a simple question, but I can't seem to figure it out from google. bcftools has 4 output options: ...