In additions to the output files listed in the cufflinks manual, cuffcompare also produces a .loci file. Can someone describe its content? Thanks.
-
-
a locus (plural loci) is the specific location of a gene or DNA sequence on a chromosome.
SOURCE: sample loci file
XLOC_000001 chr1[+]x-y - transcript_id_0
For line 1-3:
col1: locus_id (ex - XLOC_000001)
col2: chromosome[strand]location (ex - chr1[+]x-y)
col3: list of transcript_id's within gene's locus (ex - transcript_id_0)Last edited by AndrewCarpenter; 07-21-2010, 09:34 AM.
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment