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
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45 views
How to format my file using linux tools?
I have an imputed dosage for chr 22 file. its content is:
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0
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1answer
29 views
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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0answers
42 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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6
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1answer
213 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 ...
2
votes
2answers
72 views
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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0
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1answer
37 views
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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29 views
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
94 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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1
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1answer
34 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 ...
0
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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 ...
-4
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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 ...
1
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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
85 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
191 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 ...
6
votes
2answers
98 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 ...
1
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1answer
54 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?
2
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2answers
1k 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
votes
3answers
428 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 ...
0
votes
1answer
789 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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3
votes
1answer
692 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
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
46 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
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1answer
32 views
What type of information does an .sf file contain?
What is an .sf file. What information does it contain?
3
votes
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 ...
4
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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 ...
1
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3answers
675 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
votes
1answer
80 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
92 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
539 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
168 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 ...
3
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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 ...
2
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1answer
169 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 ...
4
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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
184 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
2answers
291 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
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2answers
431 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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4
votes
1answer
803 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
590 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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0answers
72 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
256 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
318 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
355 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
748 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
votes
1answer
390 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
143 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
278 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
748 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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