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Recent Replies
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
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how does it correspond to 27.2 ? or these are the other proteins ?
Comment: Merge different vcf files
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Ram
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Normalize them first using `vt normalize` or `bcftools norm` - they need to be in left-aligned parsimonious representation before you can d…
Answer: integrate single cell RNA sequencing data
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John Ma
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You need to perform batch effect removal for these. Seurat has its integration protocol, and if you use scverse on Python, the usual choice…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
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GenoMax
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I added the link for NCBI "book" since DIAMOND seems to follow the format/reporting structure for blast+ results. While the numbers shown i…
Comment: bcftools "--filter-logic" flag, what + means?
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Ram
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`PASS` + `filter_name` is `filter_name`, not `PASS,filter_name`. PASS means the locus hit no filter. You'll never see a `PASS,<something>`.…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
▴
70
Thank you for the reply ! I got seems to be even more puzzled here - we see "identities" 95% while in the example "pident" is 27.2 - so …
Comment: bcftools "--filter-logic" flag, what + means?
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Eugene A
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Thanks a lot for the explanation!
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
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Ram
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> Do you mean that because it is 1/1, so both copies is different from the reference and that is why the 0 in the AD is because no reads is…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
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Thank you !
@buchfink would you be so kind to comment ?
Comment: The famous WGS dataset, Ashkenazi Trio?
by
thadjudkins2
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As the previous poster said we’re not sure what you’re looking for, but the basic data are available at the NCBI ftp site (linked from the …
Comment: Retrieving allele-specific information for a variant using VEP annotation
by
bt_cepo
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Thank you both for your answers @masklin @ram !
For anyone facing the same problem, I followed Ram's suggestions and it worked beautifully…
Comment: how to Construct a Newick tree file from five large fasta files
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gunala.nikhil
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I need a phylogenetic tree for those 5 genomes
Comment: featurecounts not working on mirbase annotation file
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GenoMax
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What does your `featureCounts` command line looks like?
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
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lcj34
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The log file shows an error processing the key file in the FastqToReadMappingPlugin step. See the lines that contain "ERROR net.maizegeneti…
Comment: convert data frame with character column to data frame with integer column
by
Basti
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Sorry, as I indicated in my comment, we do not know what does your dataframe look like, I cannot help further without a reproducible example
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