Comments (12)
Tetrapoda will probably be the most informative for your purposes.
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but to keep is simple, for the running of the assembly itself, just stick with the default Euk database. Once you have an assembly agree that Tetrapoda will be good!
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I am using the latest docker image. Running the first command runs the pipeline all at once as it says. Should I run the annotation and the evaluation commands, or these are already run with the first command?
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running the 1st command runs the entire pipeline, including TransRate and BUSCO (with Euk database). After that, you can annotate or do whatever else you want to. Does this make sense?
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Yes, and thank you both very much for this work!
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@macmanes Another question! Can I use several samples together? Or I have to concatenate their _1 and _2 fastq files?
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@macmanes Could you please explain why is that? Biological replicates wouldn't help assembling lower expressed regions?
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@macmanes I have 6 RNAseq libraries (~35M reads each), 3 are normal 3 are not normal. Should I run 3 times the pipeline for the normal and then fuse them with orthofuser and do the same for the other 3 and then fuse the 2 merged? I have read that above 40M reads will be little to no improvement. Using 2 samples 1 from normal and 1 from not normal will it help to recall better transcripts?
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@macmanes Thank you for your reply!
These 6 samples are from 3 pairs of siblings. Do you think I should choose 1 normal and it's not normal sibling? or chose one from another family?
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