Tweet
I use some mainstream aligners (BWA, Razers3) to map human's single-end reads to hg19. And I notice that some reverse complemented reads map to the reference in the result SAM file, for FLAG is set to be 16 or 272 (256+16) in some of the alignment result. I am confused about when do the aligners reverse complement input reads and map them. Do the aligners always do this job or they just do this when a read in forward fails to map on the reference?
-
-
cross posted: https://www.biostars.org/p/170836/ -
Devon Ryan on Biostars told me that Generic aligners always look at both strands unless told otherwise. Then harold.smith.tarheel explained that this is because DNA is double-stranded. That's exactly what I was confused about.Last edited by howen; 12-29-2015, 05:18 PM.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