Comments (12)
AdamStuckert
commented on August 30, 2024
Tetrapoda will probably be the most informative for your purposes.
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macmanes
commented on August 30, 2024
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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kokyriakidis
commented on August 30, 2024
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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macmanes
commented on August 30, 2024
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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kokyriakidis
commented on August 30, 2024
Yes, and thank you both very much for this work!
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kokyriakidis
commented on August 30, 2024
@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
commented on August 30, 2024
Concatenate them all together 1st, but remember the rec for including samples. In general, we strongly recommend that you assembly 1 individual per treatment or group.
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kokyriakidis
commented on August 30, 2024
@macmanes Could you please explain why is that? Biological replicates wouldn't help assembling lower expressed regions?
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kokyriakidis
commented on August 30, 2024
@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
commented on August 30, 2024
How about this - try one assembly using my rec - concatenate 2 individuals together (1 normal and 1 not), and then do another experiment where you concatenate all the reads together. See what you get?
Matt
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kokyriakidis
commented on August 30, 2024
@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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macmanes
commented on August 30, 2024
I think I’d try for choosing samples from within a family if possible, but not knowing how different families are, it’s hard to say.
Matt
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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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Related Issues (20)
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