User: jean.elbers
jean.elbers • 160
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Posts by jean.elbers
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... Have you tried gffread - part of gff utilities (http://ccb.jhu.edu/software/stringtie/gff.shtml)? ...
written 4 days ago by
jean.elbers • 160
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... Ragout (https://github.com/fenderglass/Ragout) is also another option. ...
written 5 days ago by
jean.elbers • 160
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Comment:
C: BEAGLE 4.1 imputation
... The commands above will help you start the imputation process. ...
written 12 days ago by
jean.elbers • 160
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C: BEAGLE 4.1 imputation
... If you would like to phase and impute a VCF file, then the following works in BEAGLE 4.0 (not sure about BEAGLE 4.1)
java -Xmx4000m -jar ~/bin/beagle.r1398.jar \
gtgl=VCF-file-that-you-want-to-phase-and-impute.vcf \
nthreads=2 \
out=VCF-file-that-is-now-phased-and-imputed
*note tha ...
written 12 days ago by
jean.elbers • 160
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C: Minimum coverage for PacBio Arrow
... Thank you I will definitely consider LoRDEC or proovread initially if subsequent rounds of Pilon do not improve the protein truncatedness (new word ha!) of the assembly. I think additional rounds might improve protein truncatedness as after each round of Pilon correction, the number of corrected bas ...
written 13 days ago by
jean.elbers • 160
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Answer:
A: What is Read Group platform??
... See the following for more guidance
https://software.broadinstitute.org/gatk/documentation/article.php?id=6472 ...
written 13 days ago by
jean.elbers • 160
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... My thoughts - please take with a grain of salt. I cannot really comment on your question regarding if that means there are no paralogs in that sample because I am unaware of the target region used to design the baits. I would think that a de novo assembler such as SPAdes would potentially collapse p ...
written 13 days ago by
jean.elbers • 160
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Comment:
C: Judging best assembly
... You can also look at KAT (https://kat.readthedocs.io/en/latest/walkthrough.html#genome-assembly-analysis-using-k-mer-spectra) to assess the k-mer spectra of the reads and the k-mer spectra of the assembly. Not sure if your plant has high ploidy or not. Also important would be assessing BUSCO scores ...
written 14 days ago by
jean.elbers • 160
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... Hi,
I have 11x PacBio Sequel coverage for 2.27 Gbp (k-mer estimated) genome and was wondering if it might be enough to use PacBio's Arrow tool to call the consensus sequence. It seems possible (https://github.com/PacificBiosciences/GenomicConsensus/blob/develop/doc/FAQ.rst), but I have feelings that ...
written 14 days ago by
jean.elbers • 160
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... Have you tried BEAGLE 4.0 to see if you get the same error? Might be worth a shot. I had a similar error - sorry, can't remember it exactly, and I was able to use BEAGLE 4.0 without the error. ...
written 18 days ago by
jean.elbers • 160
Latest awards to jean.elbers
Scholar
11 days ago,
created an answer that has been accepted.
For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher
11 days ago,
created an answer with at least 3 up-votes.
For A: What is Read Group platform??
Scholar
6 weeks ago,
created an answer that has been accepted.
For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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