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Hi! Thanks for your work.
Is TrEMOLO suitable for application to the human genome?
I'm tring to detect insertions in human by TrEMOLO, but the program always stays at processing the genome.fast…
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Hi, thank you for developing cool tool.
I know that there are several posts about this but I cannot solve my problem.
I am trying to use denovo assembly with scaffold level and reference genome, u…
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Users often have a reference genome and a set of contigs. Add the option to do a nucmer mapping to the reference genome in order to order/orient the contigs into a pseudo molecule before running.
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Hi Brice,
I am using pseudo-it to produce genomes for 19 species using a single reference genome. I noticed that a species that did not sequence well is far more similar to the reference than it shou…
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Hello,
Not sure who is monitoring these issues now @satta has left Sanger, but I wasn't sure where else to send it.
Sascha showed me how to run companion on the command line using a fungidb refe…
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Hi,
During some comparisons of STAR and kallisto we saw that the number of genes/transcripts that STAR aligns to and outputs is much larger than kallisto. This obviously makes sense and is expected…
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The crash in the proteome comparison tool at the tutorial this week was a result of feature fig|1945512.3.peg.14 not having a translation. That feature derived from the genbank file https://www.ncbi.n…
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Hi,
Can someone explain to me what the -r option does in gffread?
I have read that it:
"only shows transcripts overlapping coordinate range .. (on chromosome/contig , strand if provided)"
S…
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The pseudo-autosomal regions is often annotated in the Illumina's CSV manifest as `XY` chrom. gtc2vcf probably recode them as chrom `X` in the output vcf:
https://github.com/freeseek/gtc2vcf/blob/2…
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Hi,
I have been using bcftools roh to estimate runs of homozygosity. I noticed that the individual used to generate the reference genome sequence had no roh calls, despite the fact that I have visu…