Cannot Decipher Accession and Estimate Abundance With RSEM and BAM File

[Wouter Makkinje]

Dear Sir/Madam,

After de novo transcriptome assembly using Trinity, I've used Evidential Gene to remove redundancy. This has created new accessions for each transcript, however, the original ID provided by trinity is preserved and added at the end of each transcript header. Upon using the align_and_estimate_abundance.pl tool, I get a long list indicating "WARNING: cannot decipher accession <EviGene_accession>" for every single accession. Examples of headers after using EviGene:

>NonamEVm066278t1 type=mRNA; aalen=69,48%,partial5; clen=433; offs=2-211; organism=No_name; evgclass=main; oid=TRINITY_DN69669_c0_g1_i12;
>NonamEVm035724t1 type=mRNA; aalen=104,99%,partial; clen=314; offs=2-313; organism=No_name; evgclass=main; oid=TRINITY_DN69669_c0_g1_i8;

Is it possible to just swap the accession ID created by EviGene with that provided by Trinity (oid) to circumvent this problem? And perhaps more importantly, will this provide the same/right result as transcript IDs are removed/collapsed from the original transcriptome? Or if you have another suggestion, that would be greatly appreciated.

I was also wondering whether I could use the align_and_estimate_abundance.pl tool using RSEM, but provide a previously created BAM file using bowtie2 so as to prevent performing the alignment step to save time. I've found this option to be present in the manual of the tool under --aln_method in the Trinity wiki, but (after updating trinity) this option is not present in my version (Trinity-v2.12.0, downloaded via conda environment).

Any help is appreciated!

Kind regards,

Wouter Makkinje

[Brian Haas]

Hi

I think you should be able to swap out the accessions and would then work fine.

The quant script won’t allow giving it a bam.  Try running salmon for that step. Super easy and super fast.

Best of luck 

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Brian J. Haas
The Broad Institute
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[Wouter Makkinje]

Thank you very much for the quick reply and help!

Kind regards,

Wouter Makkinje