User: jean.elbers
jean.elbers • 1.3k
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Posts by jean.elbers
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... 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.elbers • 1.3k
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... 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.elbers • 1.3k
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... 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.elbers • 1.3k
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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.elbers • 1.3k
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... 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.elbers • 1.3k
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... 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.elbers • 1.3k
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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.elbers • 1.3k
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... 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.elbers • 1.3k
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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.elbers • 1.3k
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... 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.elbers • 1.3k
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