User: jean.elbers

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Posts by jean.elbers

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Comment: C: Scaffolding a genome with long reads.
... My apologies - I actually didn't realize that Racon would fill gaps if reads span gaps in the original assembly (https://github.com/isovic/racon/issues/84) ...
written 28 days ago by jean.elbers1.3k
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Comment: C: Scaffolding a genome with long reads.
... I think you meant PBJelly (https://sourceforge.net/projects/pb-jelly/) or LRGapcloser (https://github.com/CAFS-bioinformatics/LR_Gapcloser) for gap closing instead of racon (as far as I know it's meant for polishing) ...
written 28 days ago by jean.elbers1.3k
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Answer: A: Losing reads from bam to fastq
... Maybe try `bazam` https://github.com/ssadedin/bazam java -jar /path/to/bazam/jar/bazam.jar -bam Sequences.bam | /path/to/seqtk/seqtk seq -A - > Sequences_after_mapping.fa ...
written 5 weeks ago by jean.elbers1.3k
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Comment: C: Heterozygosity in k-mer histogram
... I have never used `GenomeScope` or `jellyfish` directly, but you say your expected genome size is ~5M bp, but you apparently entered 5G bp (nine zeros instead of 6). You could also compare your results to `KAT` (https://kat.readthedocs.io/en/latest/). ...
written 5 weeks ago by jean.elbers1.3k
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Comment: C: inbreeding coefficient (F) with vcftools
... How complete percentage-wise are the called genotypes in your VCF file? What I mean is perhaps VCFtools can only calculate `F` if all samples have a genotype called for a given SNP/INDEL (aka, no missing genotypes). ...
written 5 weeks ago by jean.elbers1.3k
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Comment: C: How can a homozygous reference 0/0 genotype (GT) have a heterozygous phased geno
... Not sure how this is possible. Perhaps you should bring it up on the GATK forums or search to see if it has already been brought up? https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team ...
written 5 weeks ago by jean.elbers1.3k
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Comment: C: Maker2 Transcriptome Input
... Whatever transcriptome you end up constructing should be inputted as `altest=` and not `est=` in the `maker_opts.ctl` file if the transcriptome comes from a different species. ...
written 7 weeks ago by jean.elbers1.3k
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Comment: C: extracting strand information from BAM to BED
... I can't guarantee that this will work in all cases, but maybe try `bedtools merge -i test.bed -c 4,5,6 -o distinct|perl -pe 's/,\S+//g'`. It assumes the file in your example is called `test.bed`. ...
written 8 weeks ago by jean.elbers1.3k
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Answer: A: sequence length distribution
... `BBMap/BBTools` has a `readlength.sh` tool that you can you to make a readlength histogram of the reads after trimming. ...
written 9 weeks ago by jean.elbers1.3k
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Comment: C: Compare two sequences and obtain differences
... For FAST comparison, you could use `minimap2`, see these example instructions https://github.com/lh3/minimap2/blob/master/misc/README.md#asmvar ...
written 10 weeks ago by jean.elbers1.3k

Latest awards to jean.elbers

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Minimum coverage for PacBio Arrow
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Scholar 3 months 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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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 6 months 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 7 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Appreciated 7 months ago, created a post with more than 5 votes. For C: Racon-Illumina or Pilon?
Scholar 7 months 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 7 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For C: Racon-Illumina or Pilon?
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Scholar 8 months 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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Scholar 9 months 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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