I have a BWA alignment of reads to a small (50 kb) reference sequence. It is a transgenic sequence inserted into a host cell genome. I want to be able to locate the insert's position in the host cell genome. There are reads at the ends (pointing outwards) which have their pairs unmapped. These mates would presumably be in the flanking genomic sequence that I want to identify. Is there an easy way to get the unmapped mates? I suppose I could make a list of the reads and write a script to parse the original fastQ files, but I am hoping there is a tool already available for this (seemingly common) purpose. Any help would be greatly appreciated.
-
-
See this thread for the info you need: http://seqanswers.com/forums/showthread.php?t=12283 -
You could parse the .bam for unmapped reads whose mates mapped close to your boundaries in the correct orientation.
You could also align the fastqs to the 50kb genome and the host genome, then filter for reads that aligned to the host whose mates aligned to the insert. That's probably the best solution. You'd want the mapping position of the reads that aligned to host anyway, so this way you'd have them.Comment
-
Thanks for the suggestions. I'll look at the other thread and try your suggestions.Comment
-
Covid-19
I am confused on the issue:
the service provider company provide AmpliSeq for Illumina On-Demand, Custom, and Community Panels. for COVID diagnostic, the library was prepared, the issue started @ sample sheet, manifest file - covid- successfully added, genome (we try our level best to integrate the genome file but no use, after creating multipath the genome was integrated in sample sheet and run started, output was 93.8=Q score, Cluster passing 96.7%, Cluster density 774K) but analysis failed (Sunday) till now we try all possible methods with illumina support but no use. initially RNA amplicon was downloaded and added in sample sheet, the sample sheet was headed by DNA amplicon (no use) & now PCR amplicon was added in sample sheet but same error. plz guide.
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...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