Hi all,
I am new to pacbio, and recently working with iso-seq datasets. Take MFC7 as a example, I find there are 7 cells sequenced with 3-5kb. So I did analysis for each of them, then combine the sam files after mapping high quality cluster sequences to reference.
When I check the wiki page of cDNA primer, it seems another tool was developed for chaining GTF.
Then I think is it possible to provide all the 7 cells to ConsensusTools, and generate a big CCS file for them. Or maybe the better way is to feed all the 28 cells to tofu_warp to sizing automatically.
So, I am confused about the strategy of analysing samples with more cells for different size. It seems that I have four options for construction the FL cDNA:
1. combine all cells -> pb_warp
2. combine cells with same length -> ConsensusTools -> classify -> cluster -> collapse -> chain
3. do not combine -> ConsensusTools -> classify -> cluster -> collapse -> chain
4. do not combine -> ConsensusTools -> classify -> cluster -> merge sam -> collapse -> chain
Which one is better?
Thanks a lot
I am new to pacbio, and recently working with iso-seq datasets. Take MFC7 as a example, I find there are 7 cells sequenced with 3-5kb. So I did analysis for each of them, then combine the sam files after mapping high quality cluster sequences to reference.
When I check the wiki page of cDNA primer, it seems another tool was developed for chaining GTF.
Then I think is it possible to provide all the 7 cells to ConsensusTools, and generate a big CCS file for them. Or maybe the better way is to feed all the 28 cells to tofu_warp to sizing automatically.
So, I am confused about the strategy of analysing samples with more cells for different size. It seems that I have four options for construction the FL cDNA:
1. combine all cells -> pb_warp
2. combine cells with same length -> ConsensusTools -> classify -> cluster -> collapse -> chain
3. do not combine -> ConsensusTools -> classify -> cluster -> collapse -> chain
4. do not combine -> ConsensusTools -> classify -> cluster -> merge sam -> collapse -> chain
Which one is better?
Thanks a lot
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