Biopython fastq to fasta jobs
Seeking an experienced bioinformatics tutor to guide me through decoding DNA sequences, focusing on problematic regions like microsatellites and hairpin structures, using Python. What I Need: - A comprehensive tutoring session held over Zoom. - Beginner-level Python programming explained in detail. - Focused learning on identifying microsatellites within DNA. - A practical approach to applying Python in analyzing these sequences. Skills and Experience Required: - Expertise in bioinformatics, particularly in DNA sequence analysis. - Strong background in programming with Python, with the ability to teach at a beginner level. - Familiarity with diverse DNA data formats, including FASTA and GenBank. - Patience and excellent teaching skills. This educational ses...
...data scientist to help me predict synthetic lethality pairs using Graph Neural Networks (GNN) on my genomic data. Key Project Requirements: - Utilize GNN to accurately predict synthetic lethality pairs. - Experience with machine learning and genomics is vital. - Handle genomic data, specifically dealing with Fastq files. Ideal Skills and Experience: - Proficiency in machine learning algorithms. - Prior experience working with GNN. - Strong knowledge of genomics and data handling. - Familiarity with Fastq format datasets. Your focus should be on leveraging GNN to spot potential synthetic lethality pairs in the genomic data. The ultimate goal of this project is to aid in identifying potential drug targets and understand gene interactions in ...
...data scientist to help me predict synthetic lethality pairs using Graph Neural Networks (GNN) on my genomic data. Key Project Requirements: - Utilize GNN to accurately predict synthetic lethality pairs. - Experience with machine learning and genomics is vital. - Handle genomic data, specifically dealing with Fastq files. Ideal Skills and Experience: - Proficiency in machine learning algorithms. - Prior experience working with GNN. - Strong knowledge of genomics and data handling. - Familiarity with Fastq format datasets. Your focus should be on leveraging GNN to spot potential synthetic lethality pairs in the genomic data. The ultimate goal of this project is to aid in identifying potential drug targets and understand gene interactions in ...
...necessary data, including RNA-seq raw reads (usually in FASTQ format), a reference genome, and an annotation file (often in GTF or GFF format) that defines genomic features. Alignment: Align your RNA-seq reads to the reference genome using a suitable alignment tool like HISAT2, STAR, or Bowtie2. This step generates alignment files in formats like BAM or SAM. Feature Counting Tool: Use a feature counting tool to quantify the number of reads that align to genomic features. Popular tools include Subread's featureCounts, HTSeq, or the count function in R packages like GenomicAlignments or DESeq2. Specify Annotation File: Provide the annotation file (GTF or GFF) to the feature counting tool. This file defines the genomic features you want to ...
I am looking for someone to help me with my de novo genome assembly project. I I just need a complete guide on how to do this, because I have been stuck. Apparently I need a FASTA file and without it I cannot answer the questions I am given. I have rerun the job four times already but there is no FASTA file. I am willing to provide you with all the information needed, including what I have written this far.
I am looking for someone to help me with my de novo genome assembly project. I I just need a complete guide on how to do this, because I have been stuck. Apparently I need a FASTA file and without it I cannot answer the questions I am given. I have rerun the job four times already but there is no FASTA file. I am willing to provide you with all the information needed, including what I have written this far.
I need help building 6 gene trees. I need 6 clean, clear, phylogenetic trees built for all 6 genes. The phylogenetic relationship in the end trees s...reproducible. - here is a zip of sequences for the genes (.pep for peptide and .cds for coding file) some sequences are longer than others I aligned the files with MAFT. If you need to realign or trim files, that's alright. They just need to have the stop codons (aka. the full protein) - RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores. - I use Linux and biopython interchangeably Thank you.
I need help building 6 gene trees. I need 6 clean, clear, phylogenetic trees built for all 6 genes. The phylogenetic relationship in the end trees sho...reproducible. - here is a zip of sequences for the genes (.pep for peptide and .cds for coding file) some sequences are longer than others I aligned the files with MAFT. If you need to realign or trim files, that's alright. They just need to have the stop codons (aka. the full protein) - RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores. - I use Linux and biopython interchangeably Thank you.
We seek a...innovative MSc or PhD level bioinformatician/computational biologist to work with us to understand protein-protein interaction of processing enzymes in genetic clusters. The successful candidate will use Glide or AlphaFold to predict the interaction of two proteins. Then use that information to determine which amino acids can be mutated break that interaction. You should be able to mask regions of the receptor that should not participate in the PPI. The candidate will have significant experience with computational biology tools, genomic databases and NGS datatypes (Glide, AlphaFold, Trimmomatic, Samtools, UCSC genome browser, FASTQ, BAM). The candidate will develop data analysis plans, analyze data, and use this information to pr...
...strains. To do that you will need to identify a suitable dataset consisting of libraries of paired-end RNA-seq reads (fastq files), one for each condition/strain. How will you find a dataset? You will either 1) start with a literature search, find a relevant paper and then download the paper's data, or 2) start with a search in EBI-ENA or NCBI-SRA or GEO, find a suitable dataset and then track down the study from which it came. In both cases, you should know what the study is, what its goal and motivation was and what conditions/strains are being compared and why. Once you've found your data, in the beginning, you should have two pairs of fastq files: Condition1_R1.fastq, Condition1_R2.fastq, Condition2_R1.fastq, Condition2_R2...
Need a script that uses HISAT or STAR, and RSEM, to generate read counts from fastq files
My max budget is $50 and should be completed in 2 days. All required files are attached. I will provide 2 .gbf and 2 .gff files for reference. ,,,example2.gff. I have written a python script gbkTOgff_withbug...completed in 2 days. All required files are attached. I will provide 2 .gbf and 2 .gff files for reference. ,,,example2.gff. I have written a python script with input file , I got output of (its not complete correct, this output should be exactly match with ) Task is to create a new python script or modify file to generate correct output. Task should take multiple .gbf files as input and generate corresponding .gff files.
Fasta is a mobile application for use in public transport precisely for buses. The app function is to pin point exactly the location of the bus and yours and calculate the tine of the trajectory then come up with a pricise time the bus will take to reach you at you bus station location
...budget of $30 and need a simple script that would modify two input files: (attached are examples) to create two output files: Below are the "rules/explanations" 1. The first input file (.fasta file) has the following format: >URS0000000183_853 Faecalibacterium prausnitzii 5S rRNA XUDKDKD >URS00000040A7_1340 Streptococcus porcinus 5S rRNA YDUDIED ... This file is organized into pairs of values: Each odd line contains Name (e.g. ">URS0000000183_853 Faecalibacterium prausnitzii 5S rRNA") Each even line contains the corresponding Value (e.g. "XUDKDKD"). To create file, I need to select only those Names and Values from the file which Names are list in the "#Organism Name" column of the file:
...line of the FASTA file modification below. Multuple column flags the line if there are multiple files being processed in a folder.) 2. Looks in each of the primary subfolders for a folder that begins with medaka. if the folder contains one or more of these folders: 2a. Moves the file(s) to a new "Summary" folder, renamed. Ex: -> (ONT01.01-OFF2021.588-iNat98620869 is the folder name without the "sample_" prefix; the "1" after the iNat number indicates how many medaka folders are in the primary folder[unique number for each: 1, 2, 3, etc.]) 2b. Changes the first line text of the file from ">consensus_cl_id_32_total_supporting_reads_464_segment0 consensus_cl_id_32_total_supporting_reads_464:1.0-700.0" to ">ONT01....
...and process data files FASTQ to CRAM to BAM to Variants. The goal is to produce EXCEL compatible output. 2. Detect and compare the genetics codes to reference genomes. 3. Produce a final output results. I prefer to work in a phased manner, in your proposal submit how you prefer to divide the project in phases. I am open to the idea of a script that can automate the conversion of FASTQ to CRAM files (BWA-MEM2, GEM, etc), to BAM files (SAMTools, etc) and to Variants (BCF Tools, etc). However, the entire process should be seamless and continuous. I can provide more details upon request. **** PLEASE DO NOT RESPOND IF YOU ARE A GENERAL PURPOSE IT DEVELOPER. I NEED SOMEONE WHO HAS EXPERIENCED IN...
Hi Mohamad B., I noticed your profile and would like to offer you my project. I need to create VCF file from my single FASTQ file with RNA-seq. Thanks in advance!
This report should take FASTA file and Amino Acid from NCBI website only. BLAST should be made from NCBI website only. Description should be very detail about the genes taken, including nucleotide position numbers and all steps taken and the discussion on them. further can be discussed in a meeting.
I need you guys to complete this flow. The flow we need is 1) Allow the user to select the FastQ file (done) 2) Check validity of the file (done) 3) Align it with the standard genome (to be done) 3) Calculate the "coverage uniformity" (to be done) 5) Merge the original fastq and the standard (where the fastq is missing fill it with the standard) (to be done) 6) Select some specific genes i'll tell you (to be done) 7) Extract the selected genes in a json (i need the letters) (to be done) Check attached for step 7 and for ready made steps. URGENT! NEED TO BE DONE TODAY
I need you guys to complete this flow. The flow we need is 1) Allow the user to select the FastQ file (done) 2) Check validity of the file (done) 3) Align it with the standard genome (to be done) 3) Calculate the "coverage uniformity" (to be done) 5) Merge the original fastq and the standard (where the fastq is missing fill it with the standard) (to be done) 6) Select some specific genes i'll tell you (to be done) 7) Extract the selected genes in a json (i need the letters) (to be done) Check attached for step 7 and for ready made steps. URGENT! NEED TO BE DONE TODAY
I need you guys to complete this flow. The flow we need is 1) Allow the user to select the FastQ file (done) 2) Check validity of the file (done) 3) Align it with the standard genome (to be done) 3) Calculate the "coverage uniformity" (to be done) 5) Merge the original fastq and the standard (where the fastq is missing fill it with the standard) (to be done) 6) Select some specific genes i'll tell you (to be done) 7) Extract the selected genes in a json (i need the letters) (to be done) Check attached for step 7 and for ready made steps. URGENT! NEED TO BE DONE TODAY
I need you guys to complete this flow. The flow we need is 1) Allow the user to select the FastQ file (done) 2) Check validity of the file (done) 3) Align it with the standard genome (to be done) 3) Calculate the "coverage uniformity" (to be done) 5) Merge the original fastq and the standard (where the fastq is missing fill it with the standard) (to be done) 6) Select some specific genes i'll tell you (to be done) 7) Extract the selected genes in a json (i need the letters) (to be done) Check attached for step 7 and for ready made steps. URGENT! NEED TO BE DONE TODAY
I need you guys to complete this flow. The flow we need is 1) Allow the user to select the FastQ file (done) 2) Check validity of the file (done) 3) Align it with the standard genome (to be done) 3) Calculate the "coverage uniformity" (to be done) 5) Merge the original fastq and the standard (where the fastq is missing fill it with the standard) (to be done) 6) Select some specific genes i'll tell you (to be done) 7) Extract the selected genes in a json (i need the letters) (to be done) Check attached for step 7 and for ready made steps. URGENT! NEED TO BE DONE TODAY
Hello, we need to do a simple script in python using the bioinformatics libraries available on GitHub. The main goal is to manage the human Whole Genome Sequence. The flow is simple: 0) Allow user to select the file (fastq file) 1) Check the validity of the file 2) Align the Whole Genome to the standard reference (fasta file) 4) Calculate the "coverage uniformity" 5) Select some specific genes (see attached file) 6) Extract the "letters" of these genes 7) Save them in a JSON. If you got this, write "BIOALGORETICO"
Hi,I am looking for computational biologists who are expert in field of Metagenomics particularly Omics technologies. I need someone with skills in fastq data preprocessing .
I have GeneBank files to be converted to Fasta files. In addition, copy paste the sequences to one Word document. Around 100 files.
use one line of code to process a fale named which contains a set of DNA sequences in the fasta format for multiple sra IDS
If you a python expert, and if you have experience in biology please contact me. Otherwise, don't waist my time.
Dears, I need assistance regarding Bioconductor and Biopython. Only serious bidders welcome.
I need help to Write C++ to load and process DNA sequences in Fasta format. I will provide more details in chat.
If you are expert in python, biopython, ubuntu, then tip. Otherwise, please don't waist my time.
...Specs: Allow the user to select peptide (protein, amino acid sequence) or nucleotide sequence files in FASTA format, prompting for the FASTA format filename and sequence type (peptide versus nucleotide). Allow the user to select a matrix of amino acid substitution scores (e.g. BLOSUM, PAM(n), hydrophobicity) in the formats provided in zipped folder P1SubMatrices. You should also allow as input your PAM(n) matrix files, despite the different delimiter format. Notice the amino acid order in all matrices: A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V For input nucleotide sequences, you may find the matrix helpful, as it simulates the following nucleotide substitution matrix: A C T G A 4 -2 -2 1 C -2 4 1 -2 T -2 1 4 -2 G 1 -2 -2 4 Algorithmic Specs: Allow the use...
...nucleotides (triplet), which are either of A, T, C or G. There might be several (from 1 to 6) triplets for different amino acids. One letter abbreviation is used for amino acids e.g. A, L, K, R, I, E, D... etc (totally 20). Thus, let's say W is coded by only one triplet which is TGG, where is L is coded by 6 triplets : TTA, TTG, CTT, CTC, CTA and CTG. A gene encodes the respective protein, but the same protein can be encoded with the different codons (triplets). For every organism the frequency of each triplet for an amino acid is different (varies from 0.. to 1)! Of course, once there is only one triplet for amino acid W, the frequency for all orgamisms is just 1. But for those amino acids that have up to 6 triplets the frequencies might be e.g. 0.24; ...
Please design a profes...old example attached) It needs to show client connecting to Merchant connecting to our Onegate API that will connect them to the below and ultimately up to their Merchant or Bank Account: Acquirers: Absa Bank, FNB, Standard Bank, Nedbank, Bidvest Bank Payment Gateways: PayU, Wirecard, Onegate, Peach Payments, Iveri, Ecentric, Paygate APM's: EFTsecure, 1ForYou, OTT, Blu Voucher, Zapper, Snapscan, Mobicred, Fasta, Payflex, Masterpass, Discover Miles, eBucks, MTN MoMo, Kazang, Bitcoin I will need each Acquirer, Gateway and APM logo's in - which can be found using Google search. All of them is South Africa based offerings. This is urgent and should still award today. If your design is good, I will guide you ...
Can be discussed through DM. Having some confidential details.
...ideally need a C/C++ program to process large (1-2GB+) files. Two processes are required: 1) Search for and count the occurrences of a specific string of characters 2) Extract all lines (& adjoining information) when the specified string is identified. Input will be two files: a) A csv or tsv where each line will contain an individual string to be searched for. b) A fastq file (this is the larger of the files) which will follow a fastq format. Required output: i) A csv or tsv file which contains the string searched for and its corresponding count ii) A fastq file which contains just those rows (& corresponding information - ie the row above and two below) which contain that specific string. Given the size of the input fastq file - ...
Please see attached word application form. I need a redesign of this in word format as well as .pdf that looks appealing. Under the banks (absa, standard bank, nedbank, fnb) I also need a 5th bank added being Bidvest Bank, see logo attached. Under payment methods I need to replace Luno with just Bitcoin (see logo attached). I also need to add new payment method Fasta (see logo attached). feel free to download better copies of the logo's online
Want to build a web-based data analysis platform. Basic idea is the user visits the homepage. There is a prompt saying "click here to upload your data". After uploading, and analysis is run using linux-based open source tools. Then their results are displayed and they're allowed to downlaod their analyses. I can send you examples of similar sites with the similar functionality. Is that something you all could do? We are the National Institute of Standards and Technology. We produce reference materials and reference data for the entire US. The site we're building will be for internal use only. Behind a firewall. Won't be available to the public Content: Here is some content for the site. And an image attached iBioClo...
Want to build a web-based data analysis platform. Basic idea is the user visits the homepage. There is a prompt saying "click here to upload your data". After uploading, and analysis is run using linux-based open source tools. Then their results are displayed and they're allowed to downlaod their analyses. I can send you examples of similar sites with the similar functionality. Is that something you all could do? We are the National Institute of Standards and Technology. We produce reference materials and reference data for the entire US. The site we're building will be for internal use only. Behind a firewall. Won't be available to the public Content: Here is some content for the site. And an image attached iBioClo...
Hi We need this ad for FB and IG We want the fare zone to be as the picture we uploaded. It should be with Vectors and the main road only visible just like the image (see image 300) The zones should not be over the sea as in the picture (image 1). We need following text to be in the picture: Fasta billiga priser dygnet runt! (Gäller ej fre & lör 15.00-07.00) Use the following url for zones The colours of the zone should be the same as in Image
In the case of entire FASTQ files, this procedure should to be made for each recording of the file. So e.g. for a file of 100 records, the result should be 100 percent, one for each sign up. 1. Write a program in C that sequentially calculates the GC content of entire FASTQ files. 2. Write a program in C using an MPI library to implement while calculating the GC content of entire FASTQ files. 3. Write a program in C using OpenMP to implement it while calculating the GC content of entire FASTQ files. 4. Compare the times for the three different implementations and compare calculate accelerations for different sizes of FASTQ files (n = 100 / 10,000 / 100,000) located on github.
In the case of entire FASTQ files, this procedure should to be made for each recording of the file. So e.g. for a file of 100 records, the result should be 100 percent, one for each sign up. 1. Write a program in C that sequentially calculates the GC content of entire FASTQ files. 2. Write a program in C using an MPI library to implement while calculating the GC content of entire FASTQ files. 3. Write a program in C using OpenMP to implement it while calculating the GC content of entire FASTQ files. 4. Compare the times for the three different implementations and compare calculate accelerations for different sizes of FASTQ files (n = 100 / 10,000 / 100,000) located on github.
Looking forward to someone who has some experience with Python and Biopython. I have a finished website with a python backend. Translate the code from screenshots into the correct file so the website works with python. Some css components might be missing, they are all available online. This should not take that long to complete. Requires Python 2.7 and Biopython. Thank you.
I have a DADA2 pipeline that is finding the taxonomy of raw fastq files. It needs to be optimised to remove 2 primers, as the species detection is not to the desired level. Looking for someone who can accurately optimise the pipeline and make sure species is precise and present. You must have experience with microbiome/biological data, as the level of accuracy is important. This task needs to be delivered promptly.
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
