Tweet
There used to be an option to output all unmapped reads to a separate file, but it appears to no longer be an option. Are the unmapped reads printed to the sam file? If so, I assume there is an easy way to extract those data...if I was more proficient at scripting?
-
-
I don't know what if anything in bfast has changed, however...
If a SAM file contains both mapped and unmapped reads, you can filter this using the FLAG field. -
As maubp mentions, if you used -a3 during postprocess (recommended), you can run:
$ samtools view -f4 my.bam > unmapped_reads.sam-drdComment
-
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