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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questions
2
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1answer
38 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 ...
2
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2answers
197 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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1
vote
1answer
37 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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0
votes
1answer
17 views
What type of information does an .sf file contain?
What is an .sf file. What information does it contain?
2
votes
0answers
162 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 ...
1
vote
1answer
34 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 ...
3
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0answers
29 views
Determine reference for reference-compressed SRA file
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 internet connection. I got the "name not found ...
1
vote
3answers
180 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 ...
2
votes
1answer
63 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 ...
1
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1answer
77 views
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
<...
2
votes
3answers
183 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 ...
2
votes
1answer
132 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 ...
2
votes
4answers
933 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 ...
2
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1answer
69 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
562 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 ...
4
votes
3answers
935 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?
2
votes
1answer
124 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 ...
6
votes
1answer
121 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 (...
2
votes
2answers
272 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:
...
4
votes
1answer
313 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 ...
-1
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2answers
366 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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-2
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1answer
70 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 ...
1
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0answers
51 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
votes
1answer
147 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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2
votes
2answers
160 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 ...
5
votes
1answer
210 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 ...
13
votes
1answer
524 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 ...
3
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1answer
131 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-...
1
vote
1answer
65 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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5
votes
1answer
205 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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6
votes
3answers
401 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:
...
5
votes
3answers
279 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 ...
3
votes
2answers
580 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
votes
1answer
264 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:...
5
votes
1answer
98 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 ...
8
votes
1answer
529 views
How GFF3 attributes (9th column) varies from one gene prediction algorithm to another
GFF3 files are in tabular format with 9 fields per line, separated by tabs. The first 8 fields share almost same data structure, but the 9th field varies a lot depending on feature type and gene ...
12
votes
2answers
177 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.
4
votes
1answer
67 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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6
votes
3answers
878 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....
7
votes
3answers
1k 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 ...
12
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3answers
2k views
How do you write a .gz fastq file with Biopython?
How do you write a .gz (or .bgz) fastq file using ...
8
votes
2answers
101 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/...
4
votes
1answer
62 views
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:
...
5
votes
1answer
97 views
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 ...
5
votes
1answer
234 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
votes
1answer
411 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 ...
7
votes
3answers
465 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 ...
4
votes
1answer
147 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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10
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2answers
212 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 (...
11
votes
2answers
163 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 ...
