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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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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
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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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1answer
69 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 ...
3
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1answer
71 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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1answer
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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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0answers
33 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
67 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. ...
2
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2answers
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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
369 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 ...
2
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1answer
43 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
37 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
151 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
163 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
207 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: ...
5
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1answer
253 views

What is this 5-column sequencing format from 2009?

There is high throughput sequencing data here, and I don't know what format it is in. It was submitted in 2009, and the description says the following: Library strategy: ncRNA-Seq Library source:...
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1answer
92 views

What format is this? Pretty sure it's not a BED file

Time for guess the bioinformatics file format... :) I found this '.bed' file on GEO (GSE84660), but it's clearly not a BED file. Anyone know what it might be? And what can view it? It's from a HiC ...
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1answer
217 views

How 9th column of a gff file varies from one gene prediction algorithm to another?

GFF3 formats are tabular files with 9 fields per line, separated by tabs.First 8 fields share almost same data structure. But the 9th field varies a lot depending on the features. The last field(9th ...
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2answers
129 views

Is there a standard k-mer count file format?

I am doing a research project involving calculating k-mer frequencies and I am wondering if there is any standard file format for storing k-mer counts.
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1answer
52 views

What does the “X_OS_IND” column mean?

I want to survival analysis using the subset of TCGA LUAD dataset, which identifier are located here. ...
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2answers
306 views

How can I read FCS files using open source libraries?

FCS is a patented data format used for storing flow cytometry data. The most recent version is FCS3.1. There is some documentation on the format, but there is no information on how to read these files....
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3answers
791 views

How to convert the .vcf (imputed) file with GT:GP format to GT:DS?

I have the genotyped data from impute2 output in .gen format (imputed to 1000G P3). The file has genotype posterior probabilities (GP:3 values per variant). I have converted .gen to .vcf using qctools ...
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3answers
893 views

How do you write a .gz fastq file with Biopython?

How do you write a .gz (or .bgz) fastq file using ...
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2answers
88 views

PDB format: remark number for free text

I would like to add a text to PDB files that I'm processing with my tool, rna-pdb-tools. Someone points that the way I'm using it right now it's not correct (https://github.com/mmagnus/rna-pdb-tools/...
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1answer
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How to represent trans-spliced genes in GTF?

For example, see this gene (nad1) in ENA: http://www.ebi.ac.uk/ena/data/view/ABI60879 If you look at the XML for that gene you see the following: ...
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1answer
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Is the optional SAM NM field strictly computable from the MD and CIGAR?

From SAM Optional Fields Specification the NM field is Edit distance to the reference, including ambiguous bases but excluding clipping Assuming both the MD and CIGAR are present, is the edit ...
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1answer
133 views

Customizing bigWig file

I generate bigWig files using bamCoverage from deeptools, in part for my colleagues to visualize their mapped libraries in the IGV viewer. A problem is that the ...
6
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1answer
210 views

How should the SAM MD tag match the CIGAR string?

I am trying to understand how the MD:Z tag is used. The following is from the SAM Optional Fields Specification, which gives an example but is not thorough. The MD field aims to achieve SNP/indel ...
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2answers
236 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 ...
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1answer
94 views

What kind of “gff” format does bioawk parse?

I was wondering if I could use the gff parsing capability of bioawk to facilitate the parsing of gtf files, and I looked at the following help message: ...
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2answers
166 views

What are the de facto required fields in a SAM/BAM read group?

The SAM specification indicates that each read group must have a unique ID field, but does not mark any other field as required. I have also discovered that htsjdk throws exceptions if the sample (...
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2answers
129 views

Do variant calls change when you call from CRAM?

We're considering switching our storage format from BAM to CRAM. We work with human cancer samples, which may have very low prevalence variants (i.e. not diploid frequency). If we use lossy CRAM to ...
9
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4answers
171 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 ...
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3answers
872 views

BAM to BigWig without intermediary BedGraph

I have a pipeline for generating a BigWig file from a BAM file: BAM -> BedGraph -> BigWig Which uses bedtools genomecov ...
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5answers
192 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 ...
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1answer
921 views

What's the difference between VCF spec versions 4.1 and 4.2?

What are the key differences between VCF versions 4.1 and 4.2? It looks like v4.3 contains a changelog (specs available here) but earlier specifications do not. This biostar post points out one ...
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7answers
2k views

How to convert FASTA to BED

I have a FASTA file: ...
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3answers
634 views

Convert a BAM file from one reference to another?

I have a set of BAM files that are aligned using the NCBI GRCh37 human genome reference (with the chromosome names as NC_000001.10) but I want to analyze it using a BED file that has the UCSC hg19 ...
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4answers
10k 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 ...
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8answers
1k views

What's the most efficient file format for the storage of DNA sequences?

I'd like to learn which format is most commonly used for storing the full human genome sequence (4 letters without quality score) and why. I assume that storing it in plain-text format would be very ...