Amandine Velt - 2018-11-05

Hello all,

I have an assembled genome of 500Mb of size and PacBio 30x data to improve the scaffolding. After the scaffolding, I would like to do the gap filling step with PBJelly.

The problem is that when I use PBJelly with the default settings, it fills very well the Ns (70% of Ns are filled, what I want) but also modifies the sequences of my genome around the N (what I don’t want at all!). I just want, basically, replace the Ns with real bases, without modifying anything else.

I tried the option --capturedOnly, which doesn’t change the sequences around my Ns (perfect !), but that fills very few Ns. Only 1.5% of Ns are replaces by bases after that.

Do you know why he no longer wants to fills the Ns with the option –capturedOnly ? Do you have a solution to this problem ?

Thank you very much,
Amandine

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Here my protocol : Protocol.PBJELLY.xml

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<jellyprotocol>
<reference>/PATH/TO/assembly.fasta</reference>
<outputdir>/PATH/TO/output_dir/</outputdir>
<blasr>-minMatch 8 -sdpTupleSize 8 -minPctIdentity 85 -bestn 1 -nCandidates 10 -maxScore -500 -nproc 12 -noSplitSubreads</blasr>
<input basedir="/PATH/TO/BASEDIR/">
<job>all_corrected_reads.pacbio.fasta</job>

</jellyprotocol>

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Here my commands

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!/bin/bash

source /PATH/TO/PBSuite_15.8.24/setup.sh
cd PATH/TO/output_dir/

Setup your files

echo "Setup step" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt
Jelly.py setup Protocol.PBJELLY.xml &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt

Mapping your data

echo "Mapping step" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt
Jelly.py mapping Protocol.PBJELLY.xml &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt

Support The Gaps

echo "Support Gaps step" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt
Jelly.py support Protocol.PBJELLY.xml -x "--capturedOnly --debug" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt

Extract Useful Reads

echo "Extract Useful Reads step" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt
Jelly.py extraction Protocol.PBJELLY.xml &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt

Assemble The Gaps

echo "Assemble the Gaps step" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt
Jelly.py assembly Protocol.PBJELLY.xml -x "--nproc=24" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt

Output Your Results

echo "Output Your Results step" &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt
Jelly.py output Protocol.PBJELLY.xml &>> /PATH/TO/output_dir/log_steps.PBJELLY.txt

Provenance : Courrierhttps://go.microsoft.com/fwlink/?LinkId=550986 pour Windows 10

 
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