Is it ok to split an aligned bam by chromosome and then run MarkDuplicates on each of the files?
-
-
No in the sense you'll miss PE reads that have each read map to different chromosomes. This is a key advantage of using MarkDuplicates over the samtools method. -
I wouldn't worry about splitting by chromosome and running MarkDuplicates, in fact seems quite astute to me. Do you expect gene duplicates and this is why you are doing it? Or is it due to limited computational resources, or another issue?
I have not tried this but would be interested to see if differences occur between split-by-chr and full bams, can you report back about it if you do that?Comment
-
What do these reads tell us? That there is a gene duplication? Would you retain these? And are they common? I have not found any in my own data, and would certainly remove them. I have only dealt with 100bp PE data though.Originally posted by Heisman View PostComment
-
Ive been asked to make a pipeline run faster on a distributed system. We can parallize most of the steps (alignment, some of the gatk steps, etc) but the MarkDuplicates is quite time consuming. If I split by chormosome then run on multiple machines it gets done much faster but I don't want it to affect the results.
I am planning tests to compare the deduped bams that are produced soon. I will post the results.Comment
-
Read through this FAQ for possible tips/explanations to make it faster: http://sourceforge.net/apps/mediawik...=Main_Page#FAQ
bruce01, no idea how common they are but if you want to remove the duplicates you can't split the bam file up by chromosome, I don't think (I could in theory be wrong; I've never considered doing this).Comment
-
you will not have the exact same results. the likelihood that will affect your conclusion is pretty low, it also depends on the question.Originally posted by smleighton View PostComment
-
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 -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment