I am looking for bioinformatics colleges in Mumbai – can someone tell me which one’s are best?
I’m integrating scRNA-seq datasets from 3 different batches (different labs, same tissue type). After merging in Seurat, the UMAP clusters by batch rather than by…
I have a VCF file with ~15 million SNPs and 5000 samples (~40 GB). I need to extract allele frequencies and filter by MAF >…
I have a multiple sequence alignment (MSA) in FASTA format and I want to calculate pairwise percent identity for all pairs of sequences. I’m using…
I have a set of protein sequences in a FASTA file and I want to run a local BLAST search against a custom database I…
I have paired-end 16S V4 amplicon sequencing data (Illumina MiSeq, 250 bp PE reads) from 20 gut microbiome samples. I want to identify taxa, calculate…
I want to make my bioinformatics analysis fully reproducible using containers. My HPC cluster doesn’t allow Docker (requires root), but Singularity is available. How do…
I’m doing differential expression analysis with DESeq2 in R. I have raw count data from featureCounts. Should I normalize the counts before passing them to…
I’m assembling a bacterial genome (~4.5 Mb) using Oxford Nanopore reads with Flye. I have about 15x coverage right now. The assembly is fragmented (150+…
I have 500 novel protein sequences predicted from a de novo genome assembly and I want to annotate them with known functional domains. How do…
I want to build a RNA-seq analysis pipeline that I can share with collaborators and rerun on different datasets without manually changing paths. I’ve heard…
I have 10x Genomics scRNA-seq data processed through CellRanger. I now have the filtered_feature_bc_matrix output. What is the complete Seurat workflow from loading data to…
I have a multi-sequence FASTA file with 50,000 protein sequences. I want to: (1) filter sequences by length (keep only 100–500 aa), (2) calculate amino…
I keep running into dependency conflicts when installing bioinformatics tools. Different tools require different Python versions and library versions. How should I use conda environments…
