I'm using subprocesss.run() to run samtools command in python. The code is as below: result = subprocess.run(['samtools', 'faidx', 'hg38.fa.gz', 'chr1:169699712
I have been following the tutorial for DADA2 in R for a 16S data-set, and everything runs smoothly; however, I do have a question on how to calculate the total
I am working with phylogenetic trees. Import the phylogenetic tree file with ggtree::read.tree and get the information with readxl::read_xlsx. I want to visuali
I am running an alignment with the DECIPHER package in bioconductor using an Rstudio instance located on a server. dna1 <- RemoveGaps(dnaSet, removeGaps = "a
I have a list of about ~96,000 species names I need to collect all synonyms for. I have tried the 'taxize' package with the synonyms() function, which outputs t
First, I parsed the AAChange.refGene column from the variant_calls dataframe and then extract the Refseq ID, cDNA level change, and Protein level change informa
I'm very new to bioinformatics and RNA-seq so go easy on me. I keep getting the same error when I try perform my analysis. For background: I have a folder calle
My first time using biopython. Forgive me if this is a basic question. I would like to input sequences, then align them, and be able to refer to the index posi
Trying to implement Needleman-Wunsche algorithm for biological sequences comparison. In some circumstances there exist multiple optimal edit paths. What is th