Tweet
Is there a command line tool that would give me the nucleotide before and after a given mutation/variant base?
Thanks
-Kasthuri
Thanks
-Kasthuri
-
-
You can use samtools to do this. i.e., samtools faidx REGION -
Great! Thanks. Well, for example, it is samtools faidx filename.fasta chr1:139266-139268 (to make it easy for folks who may have this question in future). Reference fasta should be indexed first using samtools faidx.
-KasthuriLast edited by kasthuri; 01-12-2012, 04:59 AM.Comment
-
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
Comment