Hiii all ...how should I deal with fast files or vcf files that are generated from illumina re-sequencing...i want to analyze the data but don't know how to go about it..thank you
-
-
If you have both fastq (original data) and VCF (variant calls) files then someone must have already analyzed your data for you. Are you looking to reproduce that analysis?
Start here: http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29 Ask questions when needed. -
yes GenoMax..i want to reproduce the results? I am trying to use igv (broad institute) but it is giving errorsComment
-
Are you just trying to visualize the alignments/SNP's? What kind of errors are you getting with IGV?
There are several steps involved in going from the original (fastq) data to vcf files (and visualization).Comment
-
Thanks for the reply. I am trying to identify differences between reference genome and mutant genomes (SNPs and alignments). The error that I get is
File: /Users/Monika/Downloads/B768_S13.bam does not contain any sequence names which match the current genome. File: *****NC-000913-3, Genome:Comment
-
Can you ask whoever did the analysis as to what genome build they used for the analysis? Most commonly used genomes (think model organisms) are built into (or are downloadable in) IGV. Otherwise you will need to have a sequence file available with a genome name that matches the entries in the BAM file. Be sure that you have selected that genome in IGV before you open your BAM file.Comment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
Comment