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Recent Replies
Answer: Creating a local version of Clustered NR database
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Clustering `nr` is done using `mmseqs2` as noted [**here**][1] and copied below.
Be ready to have gobs of hardware available to do this.
…
Comment: Reads with highest MAPQ values from SAM files are showing mismatches to referenc
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With long nanopore reads you are going to get alignments that will have "errors" since that is partly due to characteristic of how nanopore…
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I have 30 MB of each five fasta files verticilium species genomes , actually I'm working on augustus for genome annotation of those speci…
Answer: 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
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There are already 2/3 of the seats gone. Register today and secure your place!
Comment: The inchworm process failed. Trinity running error.
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The initial `ERROR` is simply a warning so that is hopefully not the problem. What do you see when you run `java --version`?
> died with r…
Comment: The inchworm process failed. Trinity running error.
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With a sample, the error occurs in the previous step. This is the error I get with the flag --verbose
*******************************…
Comment: how to Construct a Newick tree file from five large fasta files
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1. What have you tried?
2. You need to tell us WAY more about what data you have (how large is large? is each of the 5 a single sequence?…
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When you merge 3 records, if one has filter PASS and other has filter FOO, and the third has filter BAR setting `--filter-logic x` will …
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Sure. The command is:
singularity exec -B $PWD:/phg/ /ei/software/testing/phg/1.4/phg.img /tassel-5-standalone/run_pipeline.pl -debug …
Answer: bcftools "--filter-logic" flag, what + means?
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When you merge 2 records, if one has filter `PASS` and other has filter `FOO`, setting `--filter-logic x` will return you a record with fil…
Answer: All combinations of two columns R
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Like others, I am lost what you wish to achieve. If you are really talking about regular genomic positions and intervals / overlaps etc., h…
Comment: All combinations of two columns R
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Fernando
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The expected output would be to obtein a list of dataframes of all possible combinations of df1 column 1 and column 2 and at least one comb…
Comment: All combinations of two columns R
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Basti
★
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What would be your expected output in the example you gave ?
Comment: All combinations of two columns R
by
Fernando
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For being honest, I do not know where to start with this. This is a valid example:
This would be the test df with unordered columns:
`df…
Answer: how to call variants in haploid genome
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raphael.B
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Hello, you can do this using GATK Haplotype Caller using the [--sample-ploidy](https://gatk.broadinstitute.org/hc/en-us/articles/3600372256…
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