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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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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2answers
79 views
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
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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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1answer
55 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
59 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
44 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
56 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 ...
0
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1answer
95 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 ...
4
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1answer
44 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 ...
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1answer
40 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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2answers
345 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 ...
2
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3answers
207 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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1answer
497 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
274 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
213 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
44 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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1answer
23 views
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
68 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
42 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 ...
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3answers
537 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 ...
3
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1answer
79 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 ...
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1answer
84 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
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3answers
418 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
157 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
3k 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
130 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
2k 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?
2
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1answer
165 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
240 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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2answers
373 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
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1answer
708 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
544 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
93 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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61 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
222 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
277 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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votes
1answer
330 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 ...
14
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1answer
693 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 ...
4
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1answer
329 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
119 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
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1answer
264 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
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3answers
641 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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5
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3answers
393 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
1k 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:
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5
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1answer
267 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
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1answer
103 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
788 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 ...
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2answers
236 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.
