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Questions tagged [format-conversion]

Questions relating to the conversion of one format (e.g. FASTQ) into another (FASTA).

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Fastest way to convert GTF or GFF file to a BED file?

Given a GTF/GFF3 annotation file, what is the fastest way to convert it into a BED file?
Alejandro Gonzales-Irribarren's user avatar
2 votes
1 answer
52 views

Converting .tsv to .meg for visualization

This is an add-on to the previous question I asked here. I was able to deploy a "chunking" strategy to my kmer matrix and was able to get a file with the distance measurements! From what I ...
rimo's user avatar
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3 votes
1 answer
297 views

How can I convert a BED file to GTF/GFF with gene_ids?

Given a .bed (BED12), how can I convert it to GTF/GFF formats with gene_id attributes? What is the fastest way or available tools to do it? For example, given an input like this: ...
Alejandro Gonzales-Irribarren's user avatar
0 votes
0 answers
53 views

Generate simulated bam for certain snps

I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
Shafayet Rahat's user avatar
2 votes
2 answers
375 views

Convert Symmetrix Matrix into Lower Triangular Matrix

I'm using Scipy's pdist function to calculate a distance matrix which is working great but it gives me a symmetric matrix and I want to convert it into a lower-left triangular matrix. This is what it ...
rimo's user avatar
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1 vote
0 answers
114 views

Renumbering atoms in PDB using OpenBabel

I'm trying to add polar hydrogens to protein (PDB ID 3l3l cleaned from water and ligands) and convert it to PDBQT using OpenBabel by: ...
Evgenii's user avatar
  • 11
5 votes
2 answers
389 views

Converting VCF format to text for use with PLINK and understanding column mapping

I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I'm facing the problem that I seem to be unable to use it in ...
jay.sf's user avatar
  • 173
3 votes
1 answer
377 views

Converting convert .svs files into .mrxs format

I wish to convert Aperio AFI microscope .svs files from a pathology lab microscope into 3DHistech .mrxs format. Lab ppl have some pipeline X and they asked me to look into the matter. I can read the ...
pinegulf's user avatar
-1 votes
1 answer
53 views

Variants list to aminoacids

I have the sequencing data of a Monkeypox virus sample. I have the list of variants extracted from Nextclade and I want to find the corresponding aminoacids substitution. For example I have the ...
Denise Lavezzari's user avatar
2 votes
1 answer
191 views

Arlequin - How to assign samples to populations?

I have converted a VCF file to the arlequin file format. It consists of 20 samples that should belong to three populations, along with a few thousands SNPs. However, when I load the arlequin file into ...
John's user avatar
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0 answers
46 views

Conversion FASTA to BED fails

I want to use conform-gt to get rid of some REF prefix differences see here. Conform-gt needs the reference FASTA file split by chromosome and in .vcf.gz format. How can I do this? I already tried <...
mugdi's user avatar
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0 answers
49 views

How to use a .out Kraken output format

I was given some Kraken output files but the file extension is .out. I know how to use .KREPORT files but not the .out file. Is there any way convert it to a KREPORT file or what do you recommend? ...
Miharu's user avatar
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0 votes
1 answer
302 views

convert GT:PL format to GT:GP format

I have a vcf info formatted in GT:PL. ...
Shafayet Rahat's user avatar
2 votes
0 answers
46 views

How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?

How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files? The way flow-jo exports is in wide rather than ...
Coo's user avatar
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2 votes
2 answers
2k views

How to convert fasta alignment to nexus or phylip format?

I generated a multiple sequence alignment using mafft, but I would like to convert it to nexus or phylip format (required by a downstream software). What's the easiest way to do the conversion?
Kamil S Jaron's user avatar
2 votes
2 answers
66 views

Sequence format: grouping sequences within a flat file

Is there a sequence format allowing multiple sequences to be grouped across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure. To ...
M__'s user avatar
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3 votes
1 answer
651 views

How to convert Foldseek .m8 alignment files to FASTA format?

I want to use sequence alignments found by Foldseek in PROSS. I know there are other ways to get alignments (also tried with results of HHPred), but I had in mind that Foldseek may find remote ...
O.Laprevote's user avatar
1 vote
1 answer
111 views

Convert Arlequin ("DNA" markers) to Genepop (PGDspider or otherwise)

I have Arlequin output files (*.arp) from fastSimcoal2 that I'm trying to convert to genepop files (to read into adegenet). The Arlequin files are using the "DNA" marker (50 bp long), and ...
akoontz11's user avatar
  • 123
1 vote
1 answer
731 views

How to convert multiple single-end bam files to fastq using samtools

Hi I am trying to convert bam files generated from Ion Torrent Proton sequencing to fastq format so that I can upload them to ...
Justin1609's user avatar
1 vote
2 answers
376 views

How to convert CRAM file with 10x data in three fastq files

10x Genomics data are stored in three FASTQ files, besides the standard R1 and R2 reads, there is also a I1 file with some metadata. Sometimes however they are shipped in a single bam/cram file (e.g. ...
0 votes
1 answer
754 views

How to extract docked ligands from .maegz docking results file sorted by glide gscores in Schrodinger Maestro?

My VLS run completed yielding millions of ligands and I would like to extract top-scored 20000 ligands in a separate file. Incorporating the .maegz output in Maestro is not an option as it fills up ...
Nurlybek Amangeldiuly's user avatar
1 vote
0 answers
863 views

Conversion of SAM to BAM files

I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file . The command I am using to make very ...
Aranyak Goswami's user avatar
1 vote
1 answer
207 views

Convert SNP data from GEO into PED and MAP files?

I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147 GEO provides data as SOFT ...
Dan Bolser's user avatar
0 votes
0 answers
196 views

Convert DNA raw data between a different formats [duplicate]

I have .vcf file with partly decoded genome provided by some service. How can I convert this file into other popular formats which may be used in other services? I'...
user avatar
1 vote
3 answers
2k views

Convert a fasta file to Newick format

My problem is (should be) pretty simple. I have a series of 10 sequences which I wish to convert into a Newick format file - what would be good software to do this? I've tried using Jalview and am ...
Vérace's user avatar
  • 121
1 vote
2 answers
552 views

Convert sequence in MS doc to fasta or genbank

How can I convert a sequence provided in a Microsoft doc file into a fasta or genbank format?
Peter's user avatar
  • 2,634
0 votes
1 answer
267 views

Gene expression Table to Expression Matrix converstion

I have an RNAseq gene expression file (Count data) as follows, I need to conduct a Differential gene expression analysis between Patients, for that, I need to have this file as a Matrix of Rows as ...
David's user avatar
  • 43
1 vote
1 answer
819 views

Relaxed and sequential Phylip format conversion

I routinely use AlignIO in BioPython for manipulating alignments and in context here moving from fasta format to phylip format. Alot of phylogeny packages accept a relaxed (sequence ID) & ...
M__'s user avatar
  • 12.5k
2 votes
1 answer
1k views

Converting aligned fasta to plink ped/bed

I have an alignment of multiple sequences in a FASTA file (output from MAFFT), for which I would like to simulate a phenotype using plink, but for that I need to have my alignment in a PED file or ...
Empiromancer's user avatar
4 votes
3 answers
9k views

Existing tool for converting gff3 to genbank (gbk)

I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ which can perform this task, but my files (...
Mark's user avatar
  • 143
4 votes
1 answer
991 views

How could I match atom orders between a .mol2 and a .pdb?

When I was drawing conformation of Autodock result, I noticed that Autodock generated pdbqt from dlg has some structural problem (e.g. Benzene ring missing), and wants to correct this. However I ...
march_happy's user avatar
1 vote
1 answer
53 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). ...
burger's user avatar
  • 2,199
3 votes
1 answer
3k 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 ...
Paul Endymion's user avatar
6 votes
1 answer
77 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 ...
Daniel Standage's user avatar
0 votes
1 answer
173 views

What is the `table` parameter in the UCSU ldHgGene tool?

I want to lift over the annotation from E. coli release 29 to E. coli release 42. I have followed the steps for an annotation liftover mentioned here. I got the chain file for the final step and ran: ...
Biomagician's user avatar
  • 2,459
1 vote
0 answers
188 views

How can I convert Affymetrix microarray data to bedgraph format?

I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again. I have .CEL files and I'm using the Affy ...
Min's user avatar
  • 11
3 votes
4 answers
8k 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 ...
Soerendip's user avatar
  • 1,295
2 votes
1 answer
230 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: ...
terdon's user avatar
  • 10.2k
1 vote
3 answers
6k 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 ...
beginner's user avatar
  • 631
3 votes
1 answer
6k views

How to transform a DNAStringSet from the Bioconductor package Biostrings to a data frame?

I am working on Mac OS X. I am using R version 3.5.1. I have important a FASTA file into R using Biostrings::readDNAStringSet. This creates a DNAStringSet object ...
Biomagician's user avatar
  • 2,459
6 votes
4 answers
2k views

Convert SRA to FastA

I'm trying to get the FastA files for some accessions (like NC_001416.1). I did not managed to find an FTP server or direct link to these files (I want to get it from command line with ...
Poshi's user avatar
  • 221
4 votes
4 answers
2k views

Two variants associated with same chromosomal position in genotype data for one individual

I'm trying to play around with my family's raw genetic data from Ancestry.com so that I can do some genetic analyses, and I noticed in the AncestryDNA raw data files that some regions of the genome ...
Sarah's user avatar
  • 516
8 votes
2 answers
452 views

Convert bam file to highly compressible bam

I have a large collection of bam files and I want to post-process each of them into another bam where I can make queries about: the reads position and pair-endness, insert sizes, MAPQ and other ...
719016's user avatar
  • 2,324
2 votes
2 answers
429 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 ...
Biomagician's user avatar
  • 2,459
1 vote
1 answer
207 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: ...
Biomagician's user avatar
  • 2,459
-1 votes
1 answer
461 views

Unable to Install PGDSpider using Ubuntu and wine

I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for ...
Mollie Passacantando's user avatar
17 votes
12 answers
10k views

How to convert fasta file to tab delimited file

I have a fasta file like >sample 1 gene 1 atgc >sample 1 gene 2 atgc >sample 2 gene 1 atgc I want to get the following output, with one break between ...
AudileF's user avatar
  • 955
5 votes
5 answers
9k views

How to extract / convert gff3 CDS sequences to multifasta

I would like to extract all the CDS from a batch of genomes. I have found a perl script from BioStars but this does not seem to work for me. I would preferably like to have a script/ method which will ...
AudileF's user avatar
  • 955
13 votes
2 answers
3k views

How to convert fastq to fast5

fast5 is a variant of HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract ...
aechchiki's user avatar
  • 2,676
17 votes
7 answers
6k views

How to convert BED to GFF3

I would like to convert a BED format to GFF3. The only useful tool that I could find via a google search seems to be Galaxy, ...
aechchiki's user avatar
  • 2,676