Hi, currently I have some Nanopore Direct RNA sequences. In the sequencing process rRNA should already be taken care of, although I did not perform …

Dear all, what would be the visualization tool to use to visualize multi-sequence alignment (for now 4 sequences, 20kb), perhaps with structural differences and gene …

I have run muscle with the -refine flag on an alignment of ~25k mitochondrial sequences (each around 17k in length). Unfortunately even on verbose mode …

Dear all, What software do you use to detect alternative polyadenylation from standard short-read RNA-seq? Thanks, Gregor

Hi all, I have some long reads sequencing data of Oxford nanopore technology. I mapped reads to the human genome via minimap2, mapping makes sense …

Hi biostars. I have a question regarding minimap2. For my biological problem, I am doing differential expression analysis and differential transcript usage for six (3 …

Hi, I've some Direct RNA and cDNA nanopore sequencing and would like to detect some chimeric transcript. For now I aligned the reads using minimap2 …

Dear all, i am mapping some long reads to the human transcriptome: ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz Each transcript in this reference is one sequence, and the ID contains …

<p>1: does the STAR aligner perform read clipping from 3' and 5' end while trying to re-align unmapped reads? If yes, are there any parameters …

<p>Hi all,</p> <p>when counting aligned reads that map to a gene (the exons), how do you compute the raw expression? Does an aligned read need …