Timeline for At what stage of a transcriptome assembly is it better to perform read contaminant filter?
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| Jun 30, 2020 at 22:52 | comment | added | conchoecia | Hi @Dunois - I think I was being a bit dramatic above, but yes, point #3 is specifically relevant for de novo transcriptome assembly. You'll get more accurate results if a transcriptome is only assembled from reads from 1 individual. If you need different life stages or tissue types, my suggestion is to assemble the transcriptomes from different individuals independently, then remove duplicate transcripts using orthofinder. With that being said, if you have multiple libraries from different tissues from the same individual, then assemble all those together. | |
| Aug 24, 2018 at 15:20 | vote | accept | LinuxBlanket | ||
| Aug 23, 2018 at 22:37 | comment | added | LinuxBlanket | Wow, that's a very thorough answer! Thank you very much, it seems a very clever strategy! I want to use these transcriptomes for a variety of analyses, GSEA, 3'-UTR motifs and other. | |
| Aug 23, 2018 at 15:57 | comment | added | conchoecia | Allelic differences also distort the graph with genome-based assembly, causing many misassemblies and fragmenting the output. May I ask what sort of analysis that you're doing downstream with the transcriptomes? It will only take a small amount of time to make a shell script to assemble 35 transcriptomes compared to the amount of time it will take to discover all the incomplete and incorrect transcripts if all the reads are lumped into one assembly, IMHO. I have updated the answer to give more specific instructions and the reasoning behind each step. Hope it helps! | |
| Aug 23, 2018 at 15:54 | history | edited | conchoecia | CC BY-SA 4.0 |
fixed a few typos
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| Aug 22, 2018 at 7:14 | comment | added | LinuxBlanket | Thanks for your answer, there are some interesting ideas. I want to use BLAST mainly to filter out those reads/transcript that do have a bacterial/algal hit - on my first assembly attempt, I ended up with >20kb long transcripts that were just bacterial genomes. Do allelic differences distort the graphs even with a genome-based assembly? If I assemble single individuals first, I'll have 35 individuals - not counting the pooled larvae transcriptomes, which in themselves contain 50k individuals. | |
| Aug 22, 2018 at 0:22 | history | answered | conchoecia | CC BY-SA 4.0 |