There are a number of metrics for assessment of de novo transcriptome assembly quality (eg. accuracy, contiguity, completeness, chimerism, variant resolution). Is there any software available that can generate these metrics given the assembly (FASTA) and an alignment of the assembly to the transcriptome (SAM/BAM)?
One good metric is the evaluation of transcripts with full-length (or nearly full-length) when compared to databases. Trinity RNA-seq comes with a proper script to do this. It works with any fasta file, not only with Trinity assemblies.
Best regards.
http://trinityrnaseq.sourceforge.net/analysis/full_length_transcript_analysis.html
As such there are no softwares that does the quality assessment of denovo assembly quality. If you are ok with any of the programming languages, then you can write one very easily. Importantly you need to decide on what parameters you are trying to look at and incorporate them all in one script....Hope this helps
One good metric is the evaluation of transcripts with full-length (or nearly full-length) when compared to databases. Trinity RNA-seq comes with a proper script to do this. It works with any fasta file, not only with Trinity assemblies.
Best regards.
http://trinityrnaseq.sourceforge.net/analysis/full_length_transcript_analysis.html
Ke Bi, May I please also get a copy of the Perl script you mentioned? Much thanks.
Ke Bi, May I request you to send me a copy of the script you mentioned. My email id is: [email protected].
Thanks and Best Regards
Dear Ke Bi,
I would also greatly appreciate a copy of the script you mentioned above, if you dont mind. email address is [email protected]
Kind Regards
If you have a reference genome, do evaluations based on reference genome.
Otherwise, try FRCurve. FullLengtherNext.
Dear Ke Bi,
As you mentioned above, It would be really helpful, if you could send me the script at .
Best Regards
Hi Ke Bi,
I am also working with Trinity, it will be awesome if you can send me as well a copy of your script. My email is: [email protected]
Thank you !
I dont know of a software that will give you those metrics directly. The Trinity full-length script is cool (part of the Trinity script package) and also something like CEGMA (http://korflab.ucdavis.edu/datasets/cegma/) or BUSCO (http://busco.ezlab.org/) - for estimating completeness of a conserved set of genes. TransRate is also quite useful (http://biorxiv.org/content/early/2015/06/27/021626) and Ive heard of RSEM-eval (http://www.genomebiology.com/content/pdf/s13059-014-0553-5.pdf, although I havent used this last one before). Also, measuring the percentage of the reads that map back to the transcripts will give you an estimation of whether the transcriptome represents the reads.
Hope this helps...
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools