Comparison 454vsIllumina transcripts of differents cultivars

Question

[José]

Hello, I have two transcriptomes assemblys, one sequenced with Illumina and the other with 454. I assembled separated with Trinity. The transcriptomes are from the differents cultivars of Eragrostis curvula. I perform a blast 454vsIllumina and aligned only 4000 transcripts (-query "454" 96364 transcripts -db: "Illumina" 265309 transcripts, changing the db and query the result is similar). I expected a higher value of alignments, because even though they are differents cultivars the mayority of the transcript may be similar. Now i´am running a blast of both assembles against uniprot and i`ll compare them. I don´t know if this differences is due a low coverage of 454 reads or is possible that the expression is so different. Someone performed a similar analysis?

Answer 1

[h.mon]

I wouldn't be surprised if the assemblies are indeed different: they are different cultivars, sequenced with different technologies and likely to different depths of coverage, possibly subject to different treatments / environmental conditions (you did not tell us anything about it).

Try mapping the sequencing reads to the assembled transcriptomes and check mapping rate. Also, check the quality of the assemblies, Trinity provides some tips for that on their wiki, and you could also run BUSCO.