Questions tagged [format-conversion]

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

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-1 votes
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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 ...
2 votes
1 answer
31 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 ...
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0 votes
0 answers
27 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 <...
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0 votes
0 answers
17 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? ...
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0 votes
1 answer
110 views

convert GT:PL format to GT:GP format

I have a vcf info formatted in GT:PL. ...
2 votes
0 answers
28 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 ...
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2 votes
2 answers
653 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?
2 votes
2 answers
58 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 ...
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2 votes
0 answers
177 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 ...
1 vote
1 answer
68 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 ...
1 vote
1 answer
330 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 ...
1 vote
2 answers
243 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
381 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 ...
1 vote
0 answers
462 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 ...
1 vote
1 answer
101 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 ...
0 votes
0 answers
185 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'...
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1 vote
3 answers
1k 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 ...
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1 vote
2 answers
113 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?
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0 votes
1 answer
129 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 ...
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1 vote
1 answer
559 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) & ...
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2 votes
1 answer
866 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 ...
4 votes
3 answers
6k 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 (...
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4 votes
1 answer
646 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 ...
1 vote
1 answer
50 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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3 votes
1 answer
2k 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 ...
6 votes
1 answer
71 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 ...
0 votes
1 answer
155 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: ...
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1 vote
0 answers
145 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 ...
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3 votes
4 answers
6k 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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2 votes
1 answer
207 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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1 vote
3 answers
4k 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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3 votes
1 answer
5k 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 ...
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6 votes
4 answers
1k 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 ...
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4 votes
3 answers
1k 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 ...
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8 votes
2 answers
441 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 ...
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2 votes
2 answers
375 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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1 vote
1 answer
178 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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-1 votes
1 answer
381 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 ...
14 votes
11 answers
8k 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 ...
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5 votes
5 answers
8k 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 ...
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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 ...
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15 votes
4 answers
5k 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, ...
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6 votes
2 answers
1k views

How to safely and efficiently convert subset of bam to fastq?

Question How can I extract reads from a bam file (produced by bwa-mem) to fastq given a ...
6 votes
3 answers
821 views

How to convert a binary matrix of gene presence or absence into a fasta sequence

I have a binary matrix of gene presence or absence which looks like: [roary output] ...
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9 votes
3 answers
3k views

How to convert GFF3 to GTF2

I would like to convert a file in gff3 format to a gtf2.2 format. The reason why I would like to do this is: I have a set of ...
  • 2,656
8 votes
3 answers
3k 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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5 votes
1 answer
433 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 ...
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7 votes
2 answers
2k views

How can I convert SCF trace files to ABI files?

I have a large collection of sequence trace files which are in SCF file format (binary files that in addition to the string of DNA bases also contain the electropherogram of the sample and quality ...
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17 votes
3 answers
5k 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 ...
19 votes
7 answers
13k views

How to convert FASTA to BED

I have a FASTA file: ...
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