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Hi Seeman,
I downloaded few plasmids sequences in Genbank full format from NCBI for plasmid annotation and ran the following command:
`prokka ENT2_Contig6_len_41186_circ_NDM-1_Plasmid.fasta --ou…
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
salmon
**Describe the bug**
I'm working with 15 samples, with ~5Gb total reads per sample (90,000,000 to 100,…
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Via email from MKM try the following changes:
1. Use htseq-count parameters `htseq-count --format=bam --stranded=reverse -r 'pos' --mode=intersection-nonempty $IN_FOLDER/$FILE/merged.bam $GTF > $OUT_F…
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Hello- Thank you for developing facets! This is more of a suggestion than an issue.
I noticed that reading the input pileup file with `readSnpMatrix()` takes up a substantial amount of time and me…
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Now, I am comparing several genomes using their GFF3 files. To generate a GFF3 file, I ran DFAST-core with the genome sequence of CP003989.2 (Thioalkalivibrio nitratireducens DSM 14787) as an input fi…
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Hi @tseemann
When I update my snippy to 4.6.0, I got 0 varaint after runing. snps.csv contain nothing. Please see my snps.log below
Your response is greatly apriciate !
### echo snippy 4.6.0
##…
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@satta
While running /home/xin/.nextflow/assets/sanger-pathogens/companion/bin/update_references.lua
I continuously got the following error message: "tool './bin/update_references.lua' not found; op…
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Conclusions from: #13
We found that correcting the kmer count by correction = (1-err)^k (count / correction) seems to work out fairly well.
We still need to handle the information loss from th…
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Henk has warned that it can be hard to separate outbreak samples from other environmental samples in Listeria monocytogenes, as the mutation rate is low, so there may be very few SNPs.
But Jen Gardy p…
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Hi all.
I'm doing a fairly simple RNA Seq experiment right now, but ran into a problem when trying to quantify reads from the chloroplast (A. thaliana). For the entire analysis, I am using the nf-c…