I'm currently working on trying to analyze a dataset. I'm new to the field of bioinformatics and was trying to use BWA tools, however, as soon as I re ...
I'm currently working on trying to analyze a dataset. I'm new to the field of bioinformatics and was trying to use BWA tools, however, as soon as I re ...
I have PCR-Amplified fastq files of a specific target region from several samples. For each sample, I want to know the percentage of reads that align ...
I am trying to perform Multiple Sequence Alignment using ClustalW. The code works, and I am able to see the alignments on my terminal in R. Below is t ...
I'm wondering if anyone knows any tools which allow me to count the frequency of amino acids at any specific position in a multiple-sequence alignment ...
I have a large codon alignment that has a variety of gene names in the headers. The headers are in the following format: I want to modify all of th ...
This is a two-part question: help interpreting an error; help with coding. I'm trying to run bwa-mem and sambamba to aling raw reads to ...
Given three strings: I would like to do multiple sequence alignment so that I get the following result: Using the msa() function from the msa pa ...
I am working with DNA sequence data in fasta files, and have to work only in R for this project. I do some manipulations using the seqinr package (sel ...
I want to write the first part of the Smith-Waterman algorithm in python with basic functions. I found this example, but it doesn't give me what I'm ...
I work with a Mac. I have been trying to make a multiple sequence alignment in Python using Muscle. This is the code I have been running: fro ...
I have created a sequence alignment tool to compare two strands of DNA (X and Y) to find the best alignment of substrings from X and Y. The algorithm ...
The task is to connect the input sentences which are overlapping. My problem is how to remove the overlapping parts properly. Input: first line is nu ...
I split a 52G fastq file into 10G chunks with the following code: This produced the following files: When I was attempting to assemble "outputfi ...
I have two texts, text A and text B. Text B isn't an exact copy of text A, it has a lot of special characters which aren't in text A, but it is techni ...
I have a large corpus of text, split into sentences. I have two versions of each sentence, one version has POS-tagged tokens. I want to POS tag everyt ...
I am using samtools to remove duplicates. To mark and then remove duplicates markdup relies on ms (mate score) and MC (mate cigar) tags that fixmates ...
I'm trying to write a Python3 script that performs a global alignment of two sequences, of ~ 10 kb and 11 kb length. Both are very similar to each oth ...
I have an array of traces that are look like this : Really small low part then a big High part and ended with low part again. I want to be able to ...
I want to be able to write a multiple sequence alignments using files I have downloaded in the same directory as my script. However in the Biopython C ...
I want to take two strings (DNA Sequences) and generate an alignment score. I found the DECIPHER package but that only let me generate the alignment, ...