Tweet
I have a bunch of genomes and sample reads and am looking for a way (software and method) that I can do a sequence alignment and get an output of the part(s) of the genome that were NOT covered by the sample reads. Any Ideas?
-
-
Do the alignment and then use genomecov from bedtools:
-
You can use bedtools too calculate genome coverage. Here is an example:
Comment
-
DNASTAR's SeqMan NGen will automatically create features in regions where there is no coverage as well as a coverage report that lists these regions. They also have a autoscripting tool, SeqNinja that can create new sequences from these "coverage" features.Comment
-
I just realized I never thanked you all for the help! Actually, the project that I was working on here lead to my senior research project and eventually my acceptance into graduate school! I thank you all for your help!
MarcusComment
-
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