-
Bfast jobs for analyzing AB's SOLiD data vs Illumina data
Dear Bfast experts,
I am aligning paired end reads to the mouse reference genome and the jobs exceed 40hrs for 5M short reads per parallel job.
Using unpaired option for the analysis each of my parallel jobs take < 5hrs. There are 90 such parallel jobs.
I am using the following command:
#bfast postprocess -n $(pcores -N) -U -t -f $tref -A 1 -i $baf > $sam #unpaired
bfast postprocess -n $(pcores -N) -a 3 -t -f $tref -A 1 -i $baf > $sam # paired end
Q1- Am I doing something incorrect?
Q2- I am seeking suggestions to improve the speed but not compromise on accuracy please.
Q3- Do Illumina and SOLiD paired end analyses differ - so is there a different command to be used.
Earlier when I was analyzing the mate pair library the jobs took a very long time. From the job logs the actual processing time was really lesser than that, but it seems that the jobs were stuck in a non cpu intensive process.
Thanks in advance,
Best,
bfast analyzer.
-
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...Today, 06:26 AM -
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM -
Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
Whole Transcriptome RNA-seq
Whole transcriptome sequencing...08-31-2023, 11:07 AM
Leave a comment: