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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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3answers
35 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 ...
1
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1answer
27 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 ...
4
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4answers
81 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 ...
4
votes
2answers
62 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 ...
7
votes
2answers
391 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 ...
2
votes
2answers
86 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 ...
1
vote
1answer
37 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: ...
-1
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1answer
79 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 ...
7
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7answers
2k 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 ...
5
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4answers
2k 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 ...
9
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2answers
478 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 ...
11
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4answers
1k 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, ...
5
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2answers
300 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 ...
5
votes
3answers
369 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] ...
6
votes
2answers
623 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 ...
6
votes
3answers
791 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 ...
5
votes
1answer
133 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
2answers
297 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 ...
14
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3answers
871 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 ...
14
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7answers
2k views

How to convert FASTA to BED

I have a FASTA file: ...
15
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3answers
634 views

Convert a BAM file from one reference to another?

I have a set of BAM files that are aligned using the NCBI GRCh37 human genome reference (with the chromosome names as NC_000001.10) but I want to analyze it using a BED file that has the UCSC hg19 ...