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Recent Replies
Answer: How to Identify the pathogenicity of a set of variants (by using ACMG guidelines
by
Damianos P. Melidis
▴
40
Dear DK,
Don't know if you are still interested in bioinformatics tools to implement ACMG but if you do let me share this biostars [post…
Comment: ACMG assignment tools
by
Damianos P. Melidis
▴
40
Hey, just to update with more tools:
- the wonderful* [TAPES][1]
- [vaRHC][2]
- [auto-acmg][3]
- genotoscope (see mark at the end)
Please…
Comment: Mass-spectrometry proteomics
by
Gordon Smyth
★
8.1k
limpa shares the full capabilities of the limma package, which includes adjustment for batch effects and outliers. To adjust for batch effe…
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
curious
▴
890
There are no secondary alignments as per :
samtools -f 0x100 {my_bam}
I only get secondary alignments if I add the `-a` flag to bwa …
Comment: Assemblers for short read bacterial isolates data
by
Mensur Dlakic
★
29k
Binning can be done in seconds, and there is no harm in trying it. If you run CheckM analyses before and after binning, it should give you …
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
GenoMax
151k
Can you provide the actual metrics output?
> What could be causing this?
Perhaps your data has no secondary/supplementary alignments.
Al…
Comment: Unsure whether or not I overcorrected for batch effect in dataset
by
Megan
▴
50
Thank you so much for the suggestion. I have included my code in the post.
Comment: Primer removal in amplicon sequencing
by
GenoMax
151k
`DADA2` pipeline states that all non-biological nucleotides need to be removed so choose accordingly: https://benjjneb.github.io/dada2/tuto…
Comment: Mass-spectrometry proteomics
by
Nasim Gandomdoust
•
0
Thank you for your reply. I would like to know if the package can handle batch effects and outlier samples too.
Answer: Which GWAS tool to use that can work on Czech cases and British controls, on a b
by
LChart
4.9k
There is really no way for you to do this analysis - having cases and controls perfectly confounded by populations means that every variant…
Comment: Unsure whether or not I overcorrected for batch effect in dataset
by
cfos4698
★
1.1k
It would help if you provided your code so others know what steps you took to batch-correct your data
Comment: Primer removal in amplicon sequencing
by
sxf520
•
0
Thanks. I actually want to know if I should use the full sequence (with the overhang part) or only the gene specific part as the primer se…
Comment: Primer removal in amplicon sequencing
by
GenoMax
151k
If you are looking to remove the primer sequences then you can provide these to scan/trim programs like `bbduk.sh` from BBMap suite or `fas…
Answer: GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no
by
Pierre Lindenbaum
166k
This question has been asked many times: https://www.biostars.org/p/9475152/ , https://www.biostars.org/p/146322/ , https://www.biostars.or…
Answer: Batch correction without biological covariates
by
swbarnes2
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Well, hopefully your batch variation has nothing to do with your biological variation.
If they overlap, like all your controls are one b…
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