User: jean.elbers

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jean.elbers160
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Posts by jean.elbers

<prev • 32 results • page 1 of 4 • next >
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Comment: C: bedtools getfasta (how to get only cds coding sequence)
... Have you tried gffread - part of gff utilities (http://ccb.jhu.edu/software/stringtie/gff.shtml)? ...
written 4 days ago by jean.elbers160
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Answer: A: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
... Ragout (https://github.com/fenderglass/Ragout) is also another option. ...
written 5 days ago by jean.elbers160
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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.elbers160
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Comment: 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.elbers160
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Comment: 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.elbers160
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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.elbers160
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Comment: C: Paralog detection after target capture - HybPiper
... 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.elbers160
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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.elbers160
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Minimum coverage for PacBio Arrow
... 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 ...
assembly polishing pacbio arrow written 14 days ago by jean.elbers160
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Comment: C: Beagle 4.1: Imputation - Error - ERROR: invalid ALT allele
... 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.elbers160

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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