<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">MAKER will collapse redundant evidence after alignment, so it will primarily just increase run time. The main issue with so many datasets would be false positive alignments (assembled background transcription). You can look at individual contigs in Apollo, IGV, or other browser to see where spurious alignments occur and if they are overall associated with a particular dataset (it’s ok to throw out a noisy dataset especially if you have additional data).<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 4, 2018, at 6:32 AM, Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" class="">liorglic@mail.tau.ac.il</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="rtl" class=""><div style="direction:ltr" class="">
<span style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class="">Dear MAKER users,</span><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class=""><br class=""></div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">I am new to MAKER and would like your advice.</div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">I am planning to annotate multiple genomes of tomato variants and wild relatives. To this end, I have been working on generating a diverse transcripts data set to be used as input for MAKER (along with protein sequences and the 'official' tomato annotation). My transcripts set was generated by collecting multiple available RNA-Seq results from SRA, covering diverse variants, conditions and tissues, and assembling them into transcripts using Trinity. My goal is to have a data set as diverse and broad as possible.</div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Now I have ~30 fasta files of transcripts, originating from different studies. Of course, many of the transcripts are redundant and/or partial. I am exploring ways to merge the multiple data sets into a non-redundant one, while also stitching partial transcripts into longer ones based on overlaps.</div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">However, this turns out to be not-so-trivial and I am wandering if this is really necessary in order to get a good annotation? Maybe I can just concatenate all my transcriptome assembly results, and MAKER will handle redundant and partial transcripts?</div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Can someone clarify how this works, and try to assess if an annotation based on a merged data set should be superior to one that didn't undergo such a process? If someone has actual experience with such data, that would be really helpful, but any advice would be highly appreciated.</div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class=""><br class=""></div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Thanks a lot and best regards,</div><div style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="">Lior</div>
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