Questions tagged [fasta]

should be used for questions specific to sequence file format `.fasta`. should **not** be used if you just used fasta file, or if the question is more general about sequence formats.

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3answers
74 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
21
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4answers
6k views

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this: ...
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0answers
37 views

Using BaseRecalibrator in GATK4

GATK4's BaseRecalibrator uses a list of known variants to adjust the base quality scores in a BAM file. I would like to visualize the pre and post recalibration ...
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1answer
45 views

Interpreting MultiQC plot of GATK BaseRecalibration data?

I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from ...
4
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4answers
91 views

Convert FASTA to FASTQ with dummy quality scores

I have a FASTA file which I would like to convert into FASTQ format as the tool I want to use my data in requires it in FASTQ format. So dummy quality scores are fine. Note: I am not using any ...
3
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1answer
34 views

How to generate two fasta files from samtools phase output?

samtools phase is an easy-to-use tool to phase variants from a bam file and a reference. For a sequence that has two haplotypes, like this: ...
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0answers
14 views

Obtaining HGDP project data in fasta format

I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes....
0
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1answer
19 views

SRA Toolkit and lebanese data

I am trying to extract data from this: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218 I installed SRA Toolkit, downloaded the SRR6245218 file and executed this: ...
2
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1answer
27 views

How to extract hypervariable region of mitochondrial dna from its fasta file?

Recently I've done some analysis on Human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
1
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1answer
27 views

Bedtools get fasta and ORF from a blastX run

Hello I made a blastX research (A query genome in nucleotide format translated into protein in 6 reading frames against a protein dabatase) And here is a head of ...
3
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4answers
411 views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
0
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0answers
24 views

Extract secondary structures and sequences from dssp files

I have a very messy problem and I really need your help. I have a lot of dssp files in a folder. Every dssp file contains informations about proteins. Also, I have a separate file containing two ...
1
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1answer
102 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
0
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1answer
81 views

How to edit the headers of multiple fasta files from multiple folders? (recursively)

This is an expansion of my previous question, How to edit the headers of multiple fasta files from multiple folders? My directories are organized as follows: one main directory, in which I have ...
2
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1answer
48 views

How to edit the headers of multiple fasta files from multiple folders?

My directories are organized as follows: one main directory, in which I have multiple directories that end with a number ranging from 314 to 727, followed by .3 . For example, 'mgm4761314.3'. Within ...
2
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1answer
58 views

How to convert VCF format file into Fasta(.fa) with the Reference data

I need a Software or Python Program for Converting VCF(.vcf) to FASTA(.fa) format with the help of reference (.fa)
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2answers
56 views

MiXCR: only create a single export file for all clonotypes

I am using following command from MiXCR to both align, assemble and export my input files: ...
3
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2answers
181 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
2
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1answer
57 views

Concatenate multiple fasta files into one file per unique entry

I have eight fasta files, one per gene, with 106 fasta entries per file, like this: gene1.fasta: ...
3
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1answer
147 views

How can I locate duplicated regions in a sequence?

I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
0
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0answers
21 views

return cds from a protein fasta based on gene ID in unix?

I'm trying to retrieve cds sequences for given genes. Which requires taking a list of genes gene27 gene28 Retrieving their Gene ID (LOC##) and using faa to ...
0
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1answer
62 views

Subset a protein fasta based on sequence length?

I have a strange protein fasta file. There are several entries for the same gene and I need to extract the entry with the longest width. ...
2
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1answer
42 views

how to merge two fasta based on full fasta header and remove the duplicate

I am wondering if anyone can help to merge two fasta file based on the full header as initially gene ID may be similar in some of the sequences and to remove the duplicate entry based on full fasta ...
0
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1answer
41 views

Function to find ATP binding sites

I'm currently doing a python project where I need to write code that extracts the ATP binding site from a FASTA file using a regular expression. I've tried the following code but it does not work. It ...
2
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2answers
156 views

Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?

I would like to visualize tree with multiple sequence alignment. My din.newick file is shown below, ...
2
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3answers
346 views

How to reverse complement the DNA sequences for given inverse/reverse coordinates?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt ...
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0answers
61 views

Reconstructing reference FASTA from CRAM file

I would like to reconstruct (or download) the original FASTA reference file that was used to create a CRAM file in my possession. I realize that I can download the contigs specified in the CRAM header ...
2
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1answer
53 views

Alignment for predicting DNA hybridization?

I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
5
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1answer
81 views

Is there a way to assemble contigs starting from a specific sequence?

My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
0
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2answers
94 views

Downloading Fasta for each chromosome of a complete genome

Whatever I am googling I am not able to find fasta file of each chromosome for hs37d5.fa. hs37d5.fa whole fasta file however is here ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/...
4
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1answer
821 views

Splitting fasta file into smaller files based on header pattern

I have to split this fasta files into smaller files and write them into individual files my files ...
3
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3answers
166 views

GTF from consensus sequence

I am new to using bioinformatic tools and I was hoping this community could help clear something up for me. I need to generate a gtf file. My data are a set of complete HA genes for influenza B ...
1
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2answers
40 views

Get & Annotation of isomiR (isoform of miRNA) profile from RNA-seq

I should get and analyse isomiR (isoform of miRNA) profile from RNA-seq with FASTA format. The best tool for this is "DeAnnIso". But here is a problem with this tool, it only allows you to upload ...
2
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4answers
1k 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 ...
6
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2answers
362 views

How do I re-name the headers of my Fasta file?

I appologize for asking this, but I really am really bad with regex... Can someone help me transform the headers of my fasta files from this: ...
3
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1answer
365 views

scRNA-seq, 10x cellranger pipelines

I'm starting to do sc-rnaseq using 10x cellranger pipelines, and i add TdTomato sequence to mouse reference genome and add an entry in the gtf. My code is But when I makref, it remindered that: ...
5
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1answer
123 views

How to find all variable-length seqs with an exact 5' and 3' match in a FASTA file

Context I am interested in finding all of the promotors specific to a particular sigma factor. I have identified the -35 and -10 sites from the literature, bold denotes -10, -35, binding sites: <...
2
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1answer
117 views

Question about research in bioinformatics for Computer Science student [closed]

I am a computer science student, who was interested in taking research in the field of bioinformatics. The first research idea I had was to make a model that could predict the possibility of type 2 ...
2
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5answers
1k views

How to create a .bed file from .fasta? [duplicate]

I have some problems with creating a .bed file for hg19 which I will be able to load on IGV. The fasta file contains rows of this form: ...
4
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2answers
129 views

How to align output of grep --color=always? (To QC fasta/fastq files)

Grepping out short sequences from a fasta or fastq file is a really useful way to look at sequencing data. Using the option --color=always makes this even more ...
1
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2answers
99 views

convert tRNA coordinates Result to Fasta format

I believe many of the experts here have gone through this issue, I have run tRNAscan-SE on my genome to predict all the tRNAs, and have successfully gotten all the tRNA coordinates like start, end ...
5
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3answers
558 views

finding unique headers in a fasta file using linux command line

I tried to use the following command uniq -u reference.fasta >> reference_uniq.fasta I'd like a count of the unique headers.
5
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1answer
90 views

Extracting sequences from FASTA beginning with common 5' end

I am trying to figure out the best way to extract sequences from a FASTA file which begin with a common 5' region of 43 nucleotides. Preferably, I would like to to allow for "fuzziness" in this region ...
2
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0answers
52 views

How to extract Genbank sequence and identify ORFs from the sequence in R?

I have extracted the sequence using the function ape::read.GenBank and found the function ORFik::findORFs to find ORFs in the ...
6
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4answers
504 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 ...
2
votes
2answers
79 views

How to map reads shorter than 32bp with minimap2?

I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
3
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4answers
284 views

How to merge transcript sequence with same name in a FASTA file.

Suppose we have a fasta file like ...
3
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2answers
103 views

Effect of mutation in DNA sequence on transcription factor binding sites

How much does a single mutation/alteration of a nucleotide affect the presence of a transcription factor binding site (TFBS)? I am from computer science background(Obviously). I want to make a ...
2
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1answer
364 views

How to concatenate FASTAs with respect to chromosome?

I have the following two small FASTAs, dna1.fa and dna2.fa: ...
6
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3answers
1k views

How do I rename fasta headers?

I am trying to use the seqkit replace command to replace chromosome names in the format chr_I, chr_II, ... to I, II, .... I am ...