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Giacomo Rocchetti
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Xiaokang ZH
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Recent Replies
Answer: Biopython intron-exon boundary nucleotide frequencies
by
Joe
20k
Eukaryote genomics is not a area of expertise for me so apologies if I miss some subtlety with the exons/introns here, but if the tasks is …
Comment: BED file from GSEA gene set
by
ATpoint
61k
What exactly is the question? Do you need code to make a BED file, and if so based on what? Gene symbols, coordinates of peaks? Please add …
Comment: Strange Trimmomatic behavior
by
lieven.sterck
13k
can you first confirm it is GBS data we're talking about here?
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴
380
This also shows error, Is there any way in R to arrange samples in same rows/column?
fit <- lmFit(t(mval), var)
Error in lmFit(t(mval),…
Comment: PC build for Nanopore data analysis
by
Jean-Karim Heriche
25k
I assumed that this was already covered because of the mention of
> a pipeline for the data that is subsequently generated
Answer: PC build for Nanopore data analysis
by
GenoMax
115k
I assume you are referring to MinION sequencing since other larger ONT sequencers are supplied with built in compute for doing some of the …
Comment: PC build for Nanopore data analysis
by
GenoMax
115k
ONT basecallers are [**performant only with GPU**][1]'s.
[1]: https://hackmd.io/@Miles/B1U-cOMyu#GPUs-and-Guppy-base-calling
Comment: bcftools stats: definition of indel type
by
WouterDeCoster
46k
But it requires that there is a match between a part of the REF allele and a part of the ALT allele (https://github.com/samtools/htslib/blo…
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
// i and j are the position in the alt and ref string
if ( a[i]!=END_OF_STRING && r[j]==END_OF-STRING )
{
…
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
so looking quickly an indel is when this is not a symbolic allele (<BND>) and the length of REF and the current ALT are not the same.
Comment: bcftools stats: definition of indel type
by
WouterDeCoster
46k
Yes, but I cannot figure out in which cases the INDEL type is assigned:
```
if ( *a && !*r )
{
if ( *a==']' || *a=='[' ) { …
Answer: MG RAST for Eukaryota
by
young_bioinformatician
▴
170
Hi Tom,
Yes, you can go with the predicted proteins for the annotation/downstream analysis.
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
if the type hasn't been already defined, the type is set as an array of bytes using `OR` and this function: https://github.com/samtools/hts…
Comment: arrange samples in same order in rows and column in R
by
Kevin Blighe
81k
You probably just need:
fit <- lmFit(t(mval), var)
In your model, you are also attempting to adjust for a lot of covariates- is that…
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴
380
Thank Basti, I already did this, could you please above posted full code?
Many thanks,
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