User: rhall

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rhall160
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3 years, 9 months ago
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6 years, 2 months ago
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Posts by rhall

<prev • 16 results • page 1 of 2 • next >
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Answer: A: How chimeras reads generated in PacBio?
... SMRT Bells are blunt end ligated to the DNA fragment being sequenced, even if they are in an excess there is a non-zero chance of a DNA fragment ligating to another DNA fragment before having a SMRT Bell adapter added. This would generate the classic chimera, a sequenced read being from two random p ...
written 4.1 years ago by rhall160
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Answer: A: IPD data in PacBio cmp.h5 v2.0
... That workflow isn't going to work, to align and keep IDP values you will have to use either a 2.3 style bax.h5 -> pbalign -> cmp.h5 ipbsummary on the cmp.h5 file, or a 3.x bax2bam -> pbalign -> bam -> ipbsummary on the bam file. ...
written 4.3 years ago by rhall160
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Answer: A: ERROR:PBcR Aborted (terminate called after throwing an instance of 'std::bad_all
... I would suggest assembling the 40x pacbio alone ([http://canu.readthedocs.io/en/stable/][1]) then using the other data as a validation. The hybrid approach is going to be very compute intensive, and will likely not give any better results. [1]: http://canu.readthedocs.io/en/stable/ ...
written 4.6 years ago by rhall160
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Answer: A: Run Quiver for hybrid assembly?
... As it's a hybrid assembly, my guess is that you don't have enough coverage of pacbio data to quiver correct (<30x), otherwise it would probably make more sense to do a pacbio only assembly? If you do have ~50x pacbio data then the pacbio coverage is likely more even than the illumina, as pacbio h ...
written 4.7 years ago by rhall160
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Answer: A: Sequencings of pooled BAC clones without Barcoding
... It's going to be difficult to assemble the BACs due to the overlaps, but it still may be possible. It's probably not simply a matter of HGAP settings, it will likely involve manual tweaking. You can email me directly and we can discuss in detail rhall@pacb.com ...
written 4.7 years ago by rhall160
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Answer: A: SMRT Analysis General Questions
... 1. SMRT Analysis secondary analysis software is completely self contained and does not connect / transfer any data to outside servers. It is possible to have the RS II sequencing machine be remotely monitored by pacbio for tech support purposes, no sequencing data is transferred, and it is entirely ...
written 4.7 years ago by rhall160
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Answer: A: BLASR: How to subsample alignments from a region
... I'm not aware of any software to process m4 files, but they are straightforward to parse with simple scripts, https://github.com/PacificBiosciences/blasr/wiki/Blasr-Output-Format. If you are more comfortable with sam format, blasr can output sam instead of m4, the `-sam` parameter. ...
written 5.0 years ago by rhall160 • updated 11 months ago by _r_am31k
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Answer: A: Questions about using the Celera Genome Assembler for HGAP
... The assembly failed during the 5-consensus stage. Check the [ Name ] - runCA-logs directory for the specific task failure. My guess would be in utgcns, possibly memory related. ...
written 5.0 years ago by rhall160 • updated 12 months ago by _r_am31k
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Comment: C: Tool for PacBio Denovo assembly of diploid plant genome (size 500mb) having aro
... 500 and 2500 are too low for the cutoffs, this should be calculated as the sequence length for which ~30x of you expected genome size is covered.   ...
written 5.2 years ago by rhall160
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Comment: C: Tool for PacBio Denovo assembly of diploid plant genome (size 500mb) having aro
... How many bases are in the 1-preads_ovl/preads4falcon.fasta file? Two things stand out as being things to change, if the preads4falcon.fasta file does not have >15x of the expected genome size, then the length_cutoff and length_cutoff_pr parameters should be decreased, this will be dependent on yo ...
written 5.2 years ago by rhall160

Latest awards to rhall

Scholar 4.1 years ago, created an answer that has been accepted. For A: How PacBio quality is calculated?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: PacBio data assembly with Celera
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: PacBio data assembly with Celera
Scholar 5.6 years ago, created an answer that has been accepted. For A: How PacBio quality is calculated?
Scholar 6.2 years ago, created an answer that has been accepted. For A: How PacBio quality is calculated?

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