After a struggle to get samtools successfully installed and working on my windows machine, I'm now having trouble (I think) indexing a bam file. I'm using cygwin to use samtools. I'm planning on visualizing a metagenomic sequence for SNP screening in IGV but the bam file format isn't supported. A message pops up saying that the bam file needs to be indexed. In samtools I'm using ./samtools sort <file.bam> <file.sorted> and a sorted file is successfully made. However when I go to index the file using ./samtools index file.sorted.bam a 24kb file is made. Is there something I'm doing wrong here? Thank you all for your help so far.
-
-
IGV supports .bam files. I look at indexed .bam files all the time on IGV. It woud be rather useless software if it didn't handle .bams. 24 kb sounds about right for the index. Make the index, then try to load the .bam into IGV. -
IGV will also index them for you if you do not have one.Comment
-
When I try to load a .bam file it tells me it needs to be indexed. Do I have to load both the .bam and the index simultaneously?Comment
-
No, just load the .bam. IGV will lok for a .bam.bai with the same name in the directory with the .bam, and when it finds it, it will work.Comment
-
Thank you for your help guys, I got it to work.Comment
-
Hi,
I'd like to make a slight correction for the benefit of future googlers. IGV will not create an index for a BAM file, although we might add this in the future. Use samtools or Picard to create such an index. It will index a SAM file for you, that is an IGV specific index created before the BAM index spec and implementation were finished, i.e. a long time ago. We keep it for backward compatibility, but it is not the same index as the BAM file index.
JimComment
-
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...Yesterday, 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