Hi All, I was wondering if someone could maybe weight in on an 'issue' I'm having. I've been using Translate a lot recently (great program), running lots of different assembly variants (some are TPM filter, some TransRate filtered etc, etc).
Now a consistent issue I've been having is the initial generation of the .bam file. It takes a long time (not suprising since its a massive transcriptome), but once the .bam completes (presumably) TransRate gets stuck, never moving past the .bam and/or onto the downstream analysis. Its not a massive issue, since cancelling the run, then restarting will progress the program to completion.
I wouldn’t think much off it but some of my results recently have been ‘interesting’. My best transcriptome’ initial score rated 0.8, whilst the good.assembly 1.5. Is it even possible to get TransRate scores >1? Certainly I’ve improved my ability to construct good transcriptomes as of late, but I’m more inclined to think somethings going wrong in the analysis. Should I be trusting these scores or is TransRate getting stuck affecting the outputs?
Good morning. I've made a couple of assembly with a mixture of single- and paired end reads. The question of SE_reads came up earlier, e.g. here:
@preeti333 : yes, this is currently restricted to paired-end data. The information provided by single-end data is much less useful and reliable for assembly evaluation.
I've installed transrate on my mac to assess the quality of different assemblies. Everything seem to work fine for the contig metrics (2sec for 38K contigs ranging from 200-15000bp). This effectively run either with example data or my own assemblies. However, when I tried to run the read mapping metric analysis (with example data or my assemblies), no (INFO) lines appear below my command line, Additionally Salmon PID seems to run in loop with really memory usage in TOP (99-100% USAGE / 532K memory) and the Global CPU usage is not more than 5% in the activiy monitor. I've tried to move the transrate folder in other locations with no success. Could you please help me on that.
scorecolumns show the scores for the different assemblers, and the
optcolumns are the optimal scores.