Detecting random distribution of reads in ORF from the assembled transcripts

Question

[seta]

Hi all,

I read in a paper (http://www.ncbi.nlm.nih.gov/pubmed/25881092) that the authors assessed the sequencing bias via detecting random distribution of reads in ORF from the assembled transcripts to evaluate the assembly quality. Could anybody please let me know how I can do such a assessment?

Thanks

[Michael]

you need to link 'a paper', while waiting for answers read the Methods section of the paper.

[seta]

Of course, I read material section, but has not been mentioned.

Answer 1

[Michael]

You are referring to Figure 1b? http://www.biomedcentral.com/1471-2164/16/298/figure/F1

This is just the number of reads over the relative read length. Divide each predicted ORF into 10 equally sized bins, count the reads in the bin, and sum up the bins. They use this only to show that there is no positional bias in ORF coverage.

[seta]

Thanks Michael. Is it possible to help me for the required commands or tool to this task?. In your professional view, this parameter is really of the criteria of high quality assembly?

[Michael]

Well, that's quite easy to build in R, what's your input data? You need to map back reads to contigs in BAM/SAM format, ORF coordinates on contigs in GFF format. If you want help with your task you need to post example data and what you have tried already.

[Michael]

With respect to how good this is to evaluate an assembly, I think it doesn't show much at all.

[seta]

OK, Thanks for your comments