Biostar

12,219 results • Page 1 of 245

I have some FASTA files with a lot of sequences inside each one, but I need to have just one file with all of these senteces inside it! How...I have some FASTA files with a lot of sequences inside each one, but I need to have just one file with all of these senteces inside it! How can...I merge this files without losing FASTA formatting

fasta sequences

updated 6.9 years ago • l.souza

number is too high. Therefore I would like to concatenate the contigs for a given species reference fasta file into ~30 contigs. I believe I could use code such as below to merge all the contigs into one: > grep -v "^>" test.fasta | awk...BEGIN { ORS=""; print > ">Sequence_name\n" } { print }' > new.fasta However I would like to merge them into ~30 c…

fasta merge contigs

updated 4.9 years ago • Rubal

Hi all, I used the ***bedtools merge*** function to make a bed format file with merged ranges. What I'd like to do now is convert that to a fasta file. The ***bedtools...getfasta*** function will only extract from the original fasta and not make the merges from the merged.bed file. Any suggestions as to how to get a fasta from the merged.bed file? I've

fasta bedtools

updated 24 months ago • zhousun21

Hello, I want to merge a set of .ffn files into one single fasta file. Thanks

fasta ffn

updated 3.8 years ago • alexa.fitzpatrick

I have a fasta file that contains sequences like so : >PT_TAC_1 ATGCATGCATGC >PT_TAC_2 ATGCATCGATCG Following BLASTx, i obtained...is in the other, like so : ID Description PT_TAC_1 Some_unique_description How do i merge the description so as to result in a fasta file containing : >PT_TAC_1_some_unique_description ATGCATGCATGC

perl blast fasta

updated 12.1 years ago • Torque_Cloud

5.64e-14 73.6 cluster_14420 SYMC_XENLA 50.676 961 408 13 4 956 2 904 0.0 935 Whats the best way to merge the annotation result with the fasta file so I have it looking like this >cluster_9694 SFR1_HUMAN MEGVNARNVVLNKGPQQMSSSLKDRLKRCGRYYSSPTTPKPSIGFLPTPDSSAASSQSLNLDCPTPTCDNGPVSETPPSTILTPSSSDKHGDSTFDDSSSLSCSTPVLKVRDSQGSHPRVKRLRLSSQACFKVQFPPESNSGRGENHPKQQVLNSSLLEDSISEISTCDDKTEADVNSPEKVQPTIT…

next-gen genome

updated 3.4 years ago • nidhi.vijayan

44.fa ch2.fa_16903_17204-2-46.fa ch2.fa_16903_17204-61-47.fa ch2.fa_16903_17204-73-52.fa I want to merge files with the similar beginning (ch14.ta_20452_206652 or ch2.ta_16903_17204) into one fasta. Tried to do it manually

merge

updated 3.9 years ago • PoGibas

I've been trying to merge separate fasta files into a single file. I use `cat *.fasta > outputname` but every time I do it I lose some of the headers, which...I've been trying to merge separate fasta files into a single file. I use `cat *.fasta > outputname` but every time I do it I lose some of the headers, which is puzzling. Example: File1 ``` >scaffold001 AGTCATGAT ``` …

fasta linux

updated 13 months ago • esterbuiate

I would like to ask how to merge different fasta files into one fasta file and name each contig according to the name of the original fasta file? For example...gene1.fasta, gene2.fasta, and gene3.fasta are merged into gene.fasta, and the contig names in gene.fasta are >gene1, >gene2, >gene3

fasta merge

updated 2.2 years ago • zhichusun

I have a fasta file with CDS of a viral genome. These sequences are in order. By utilising the ids "fig|11292.9703.CDS.1" Both the problems...are separate 1\. I want to merge these genes to form a whole genome? I mean firstly I want to merge all the corresponding CDS into one big genome and then...next fasta file should start like ``` >Genome_1 ALL THE CDS COMBINED >Genome_2 A…

fasta linux genome

updated 13 months ago • iankeetkumar

gt;seq_10 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT I would like to merge some of the fasta sequences based on IDs Output: >seq_1_seq_2 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTCAAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

fasta sequences

updated 2.8 years ago • Lu K

I have a series of assemblies in fasta format from SOAP2 using different k values. I would like to merge the resulting assemblies to one file because some k...I have a series of assemblies in fasta format from SOAP2 using different k values. I would like to merge the resulting assemblies to one file because some k values assemble parts that others don't, to create hopefully larger contigs. I thou…

assembly

updated 10.4 years ago • rob234king

Hello, I am going to download fa files by chromsome from UCSC Eventually I want to get a single fasta file. So I have to merge them together. How to merge fa files into one fa file? How to convert a fa file to a fasta file? Thanks

fasta sequence

updated 12.8 years ago • Zhshqzyc

Hello, I have genotyping data converted to plink files (binary files) that I want to merge. Before merging, I would like to align it to an human genome reference (that I have in fasta format) to avoid problems arising

Plink alignment fasta

updated 19 months ago • 818fd56e

Hi, I have two multifasta files. I want to merge them deleting all those fasta seqences from the first multifasta file which are also in the second file. I need to do it

Assembly genome sequence bcftools fasta

updated 7.8 years ago • Pawel Osipowski

I have a .fasta file containing multiple sequences. and I have a separate file containing some description of each of the sequences...in the .fasta file. how to merge them

header fasta

updated 20 months ago • manaswiniparija3

Hello! I have two fasta files; 'fasta_a' contains gene names, and 'fasta_b' contains gene names, sequences, lengths, paths, etc. If the gene name from...thank you in advance for your help! fasta_a_dict = SeqIO.to_dict(SeqIO.parse(fasta_a_path, "fasta")) fasta_b_dict = {rec.id : rec.seq for rec in SeqIO.parse(fasta_b_path, "fasta")} for key in fasta_a_dict: if key in …

python fasta biopython

updated 5.6 years ago • js8226

Hi all, I actually have two fasta file candidates_aa_0042.fasta and candidates_aa_0035.fasta and two dataframe Best_blast_candidate_hit_0042.csv...Vollenhovia emeryi] 411798 Vollenhovia emeryi Eukaryota Hymenoptera And I actually have to merge them BUT in the same order than the seqID in the fasta file. For exemple if the fasta file 1 contains : >seq1_0035_0042...ATGGAGAGATAG …

pandas python merge

updated 5.9 years ago • Chvatil

Hi anyone has an idea about merging multiple `.fasta` flies retaining the file headers? I tried `cat` command but it will only keep the 1st header. What I want

Assembly sequencing

updated 4.0 years ago • Azuretimes

practice and got this problem stuck! I downloaded h19.chromFa at ucsc and now am trying to sort and merge it by chromosome number. I used the code below from this blog https://digibio.blogspot.com/2014/07/sort-and-merge-fasta

sorting fasta

updated 4.7 years ago • woojoy14

Hello, I want to merge fastq pair ends (R1 and R2) files to obtain one file that i can run on seqtk to end up with the fasta file of my sequenced isolate...Only problem is am not sure hot to merge R1 and R2 files. what is the best way to do it ? Thank you

Illumina fastq seqtk

updated 3.0 years ago • HT

Hii, I have a merged fasta file of 1500 sequences.I want to split it into only 2 files ,one having 1000 fasta sequnces and other having 500...fasta sequences with headers intact.Can anyone suggest me the way with proper command to do it easily by awk or grep

alignment sequence

updated 4.0 years ago • priya120195

genomes of all known and sequenced human > viruses obtained from NCBI (as of Sep 2015), and merged them into one > file (referred to as the "viral reference file") in fasta file format. > Merge all virus fasta file into...one big fasta file called viruses.fa Reference for the above citation: GitHub viGEN tutorial I'd like to know what's the appropriate...way to merge files …

RNA-Seq viral genome RefSeq fasta fastq

updated 3.3 years ago • MatStat

I am using FastaAlternateReferenceMaker to generate fasta reads with the indels I have in a VCF file. I am also using a bed file becaouse I need to create fasta reads from the specific...I am using FastaAlternateReferenceMaker to generate fasta reads with the indels I have in a VCF file. I am also using a bed file becaouse I need to create fasta reads from the specific start and end positions. I…

FastaAlternateReferenceMaker

updated 9 weeks ago • ManuelDB

I have denovo assemblies from cufflinks in .gtf format and assemblies from Trinity in .fasta format. I want to merge both assemblies. How can I convert fasta to .gft format? Thanks

Assembly

updated 7.4 years ago • mike

calculate the coverage of my reads against this database using bowtie2 for mapping , for that , i merge all the genomes sequences i downloaded from ncbi in one fasta_library ( i merge 74 files in on fasta file ) , the problem is...that in this fasta file (the library i created ) i have a lot of duplicated sequences , and that affected the coverage in a big way , so i'm asking...if theres any w…

Assembly alignment sequencing assembly

updated 4.0 years ago • Bioinfo

Hi all, I have fasta files containing sequences from different loci (one fasta file per individual) and would like to change the headers...to then merge everything into one big fasta file. This is the format of the first two lines of one my fasta files (called individual1

fasta

updated 12 months ago • Zoe

I have two relatively large FASTA files of ESTs that have similar sequences in them, but they have different IDs. I wish to cycle through every sequence...in file A and find the corresponding sequence in file B if it exists. However I do not wish to merge the files, merely identify corresponding sequences and extract the respective IDs for each file. This way I could analyse

duplicates fasta

updated 10.0 years ago • gtho123

using the NCBI BLAST 16s bacteria and archaea database. For each sample I have a forward primer fasta sequence (7F) and a reverse primer fasta sequence (1540R). For ~40 I have a 'spliced' sequence which contains a fasta with a merged...do not have a 'spliced' sequence. My questions are: 1.) Is there a best practice protocol for merging forward and reverse primers? 2.) Can I concate…

16S taxonomy rRNA microbiology primers

updated 2.8 years ago • ddowlin

Hello, I have 22 VCFs with every autosomal chromosome , all aligned with BWA MEM and UCSC GRCh37 fasta from the same fastq files (paired end). Source is a Whole Exome Sequencing x30 (illumina chip) generated with samtools...Hello, I have 22 VCFs with every autosomal chromosome , all aligned with BWA MEM and UCSC GRCh37 fasta from the same fastq files (paired end). Source is a Whole Exome Sequen…

vcf bcftools

updated 5.7 years ago • miqrom

T 0 -M 0" The resulting file was still large with around 1.3M contigs and 1.6GB. How can I merge these remaining contigs more? When I annotated this 1.3M contig fasta I had multiple repeats for almost all genes, so...there has to be a more concise way to merge similar transcripts together. Can someone help me out with this problem

cd-hit fasta Assembly RNA-Seq

updated 8.4 years ago • satshil.r

mapping transcriptomic data In order to do this, I have the 2 .fa files and the 2 .gtf files For fasta files, I can easly merge the files cat file1.fa file2.fa > file1.2.fa And for gtf files? What can I do? Thanks for the help

reference genome

updated 3.8 years ago • GiuliaAC

I am currently working with my professor and have been asked to convert some FASTQ files to FASTA. There are several files and each of them are split into 2 (R1 and R2), correct me if I am wrong, but I believe these are called...Illumina sequences? Do I have to merge these files or can I convert each of them to FASTA files separately? I would like to know what your suggestions are on a...good w…

FASTQ FASTA Conversion

updated 5.0 years ago • Khosh.0

I have fasta sequence of sacCer3 strain of yeast downloaded form http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/chromosomes...Because I need to mapping mu sequence data to this specie, I have to merge them together. Could you tell me how to merge them ( chrI.fa, chrII.fa, chrIII.fa ...) ? May I cat them all together directly by

RNA-Seq sequencing

updated 4.7 years ago • Ashley

Merge reads1 and read2 by using shuffleSequences_fastq.pl script: > perl shuffleSequences_fastq.pl Read1.fastq Read2.fastq...ReadsMerge.fastq Now how to convert paired end fastq file into fasta format correctly

fastq fasta ngs

updated 7.3 years ago • Abdul Rafay Khan

Hi! I am having issues with multiple genes (fasta files) which i am supposed to concatenate. My issue lies in that all these genes have identical taxon-identifiers, meaning...in the combined file. What i am wondering is if there is any method, preferably in python, to merge all sequences with a identical header into one sequence (ie. remove the duplicate header entries, and then merge all seque…

sequence

updated 5.5 years ago • hugo.swenson

Hi, I am following the link: http://amos.sourceforge.net/wiki/index.php/Minimus2 for the merging of two contig files from velvet. It is written on the link: "......for merging one or two sequence sets (S1,S2)." here, do sequence...sets mean contig files in fasta format? I am facing the following error during merging: command is: ./minimus2 all_velvet -D REFCOUNT=213048 error: ``` The…

Assembly software-error

updated 20 months ago • waqasnayab

stringtie **Objective is to compare A vs B for sample1 and A vs B for sample2.** How should I merge the assemblies using `stringtie --merge` ? Should I merge assemblies separately for sample 1 and sample 2 or both of them...together? i.e. while running `stringtie --merge`, should I run in twice; once with a **mergelist.txt** file for sample1 and then for **sample2

RNA-Seq stringtie merge transcriptome assembly

updated 7.0 years ago • lakhujanivijay

I have two fasta files of DNA sequences for upstream promoter regions for two species, and I would like to align them in clustalW I read...I'm trying to understand if that means I need to have each orthologous pair, one after the other, merged into one fasta file for my two species. And does anyone know how this can be achieved

Fasta Clustal

updated 15 months ago • burnsro

Hello, I have a question regarding merging the BAM files. I have several libraries 4 lanes each. I demultiplexed, mapped against the reference genome, gave the...read group name, merged libraries using samtools merge and removed the duplicate reads. Now that I did variant calling I realised I have a call...for 4 libraries separately, that is because I did read group name before merging. Is this …

BAM merge readgroupname

updated 3.6 years ago • User000

Hi Appreciate any advise or links if it was discussed before. I merged multiple fasta files into one big fasta file (>2M sequences) and when i try to do alignment using mafft, first of all, it...secondly, it produces output with 0 size. I tried to use muscle but it appeared it cannot handle fasta files with too many sequences. What are my options to perform alignment of so many sequenc…

alignment

updated 4.0 years ago • FionaK78

Hi, I have a fasta file, which has some same headers like below. They have different sequence but same header. How can I merge them or what

genome sequence

updated 20 months ago • Mehmet

I have 10 consensus sequence files which have some overlapping regions between them. I would like to merge all of them to generate single consensus fasta file. I have looked into emboss merger but it takes only two input files

assembly consensus

updated 5.6 years ago • kspata

I have a set of proteoform sequences that originate from many proteins from the same organism in fasta format. I am wanting to effectively remove the duplicates at 100% similarity but I would like to merge the headers from...I have a set of proteoform sequences that originate from many proteins from the same organism in fasta format. I am wanting to effectively remove the duplicates at 100% simil…

protein header duplicate peptides sequence

updated 16 months ago • katieostrouchov

Hey Guys, I'm having a problem trying to extract the transcripts from a merged StringTie .gtf file with gffread. I have downloaded the cDNA fastq file from ENSEMBL and tried to run the following...Hey Guys, I'm having a problem trying to extract the transcripts from a merged StringTie .gtf file with gffread. I have downloaded the cDNA fastq file from ENSEMBL and tried to run the following com…

gffread gtf fasta

updated 2.4 years ago • Vitor1

Hi, I have protein fasta file whose headers look like '>evm.model.chr.9.52'. There are almost 30k+ proteins. I have performed functional annotations...to gene structure we get from EVM. The thing is, in that files I had columns so I basically merged information. Now, I al performing some analysis and I want to add atleast protein name or even GO term in fasta header

protein fasta functional-annotation header

updated 14 months ago • ahmadjoyyia

Hello, Everyone !! I have an easy one , I am sure I am missing something here. I am trying to merge a number of vcf files to one large vcf, utilising bcfttools merge. the command I used is following where is Samples is the...Hello, Everyone !! I have an easy one , I am sure I am missing something here. I am trying to merge a number of vcf files to one large vcf, utilising bcfttools merge…

bcftools next-gen vcf

updated 5.2 years ago • abdulbenissa

Hey all! I have a very easy task to do with my sequences but my knowledge on managing fasta files by bash command is not big enough to deal with this :( I'd truly appreciate your help with this. So to the point, this...Hey all! I have a very easy task to do with my sequences but my knowledge on managing fasta files by bash command is not big enough to deal with this :( I'd truly appreciate yo…

fasta bash sequence concatenate

updated 4.5 years ago • c_gomez

Is it in order if I convert the bam files(obtained by mapping to reference) to fastq files, merge the paired reads, then convert the fastq files to fasta format? The idea is to get fasta files from the reads for feature...prediction purposes. If that is the way to do it how to one get continues fasta sequences , since on following the mentioned step I get something like this: >HWI-574/…

bam protein-coding genes fastq fasta paired-reads

updated 6.9 years ago • chevivien

from ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/. Now I would like to merge the content in ptt files to the fasta header line for each corresponding protein sequence. The only thing that is common

python fasta ptt file

updated 7.1 years ago • Promi

12,219 results • Page 1 of 245

Recent Votes

Answer: Rename multiple fastq.gz files

Comment: VCF to human friendly form?

Comment: Integration of transcriptomics and proteomics: difficult matchin names

BRAKER3 genome annotation

Answer: read depth using samtools

Answer: BRAKER3 genome annotation

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