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Answer: Biostar handbook
by
GenoMax
150k
There is no hard copy available AFAIK. After purchasing a license you get access to a PDF (in addition to the online version) that you coul…
Comment: Addressing two nuisance factors in RNAseq
by
jared.andrews07
★
18k
Yes, that is what they're suggesting, as it is the simplest model for what you want (and makes the `RNA_extraction_day` and `library_prep_d…
Answer: pangenome - Create a diagram venn
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mplace
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I used supervenn, makes a nice easy to read venn alternative
"https://github.com/gecko984/supervenn"
Comment: Addressing two nuisance factors in RNAseq
by
jkim
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Thanks, ATpoint. But I'm not sure if I understand your suggestion. Are you suggesting the following design?
```
| sample_name | treatment …
Answer: Addressing two nuisance factors in RNAseq
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ATpoint
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You have an extraction core? That's awesome.
Anyway, why not keeping it as a single blocking factor. The samples extracted as A get preppe…
Comment: DRAGEN FILTER
by
GenoMax
150k
Equivalence of commands in the two modes is discussed in the first link above. Did you check that?
Comment: DRAGEN FILTER
by
theresia.celine
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Hi, thank you for the information, I already obtained my VCF file with the default filter, but I'm questioning the reliability of this defa…
Comment: DRAGEN FILTER
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theresia.celine
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Hi, I'm using DRAGEN 4.2.7, which perform DRAGEN-ML, that's why the default filter is QUAL > 3. But I'm still wondering if this threshold i…
Comment: DRAGEN FILTER
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Which DRAGEN version are you using? The filtering heavily depends on which DRAGEN version and commands you have used.
Comment: DRAGEN FILTER
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DRAGEN uses an optimized version of GATK. See --> https://gatk.broadinstitute.org/hc/en-us/articles/4410456501915-Functional-equivalence-in…
Comment: How to check normal BAM_files before create a Panel Of Normals (PoN)
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AIMAR
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I've 12 normal samples. Thanks for the share
Comment: How to check normal BAM_files before create a Panel Of Normals (PoN)
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AIMAR
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Understood sir.
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> However I got 0 significant contig.
That alone does not necessarily indicate a problem. There could in reality be non differences, or no…
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Jorge - Ensembl
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Hi! [Transcript naming][1] is part of the [Ensembl gene annotation pipeline][2]. There will be further review for species [annotated both b…
Comment: How to check normal BAM_files before create a Panel Of Normals (PoN)
by
GenoMax
150k
Do you have enough samples to create a private PON? GATK recommends a minimum of 40. If not you can use public 1000 genomes PON.
https://g…
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