I used Magic-BLAST to align EST Sanger reads to a reference genome. Is there a program available that can assemble these alignments into transcripts that will take SAM/BAM format as input? I assume assemblers designed for RNA-seq (Stringtie, Cufflinks, etc.) can't accommodate long-read alignments, at least not accurately. Is this the case?
The PAVE (Program for assembling and viewing ESTs) system has been created for large projects with multiple libraries. This allows comparing across libraries for differentially expressed genes, which will become more relevant with the large number of ESTs generated by the next-generation sequencing machines. The PAVE system also has a web interface, which allows extensive querying ability on the libraries.
Reference:
Carol Soderlund, Eric Johnson, Matthew Bomhoff, Anne Descour (2009) PAVE: Program for assembling and viewing ESTs. BMC Genomics. doi: 10.1186/1471-2164-10-400
Hi Christopher,
if you obtained a BAM/SAM file after running Magic-BLAST you could perform a reference guided transcriptome assembly. My suggestion would be to use Trinity, which can perform both de novo and reference guided assemblies (https://github.com/trinityrnaseq/trinityrnaseq/wiki/Genome-Guided-Trinity-Transcriptome-Assembly). You may have to tune some parameters like the minimum coverage because if you are starting from ESTs you will have low coverage.
In any case also stringtie2 should be able to deal with the data that you have generated however it is not going to produce an actual assembly but only a genome annotation from which you could extract the FASTA file of the transcripts with other tools (like gffread from the cufflinks package).
I hope this helps!
Riccardo
Scientific Director
www.sequentiabiotech.com
Hi Colleague
Find the following URL may help you:
Article PAVE: program for assembling and viewing ESTs
Regards...
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