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Recent Replies
Comment: Expanding reference genome with alt loci and decoy sequences
by
appropiate
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30
Thanks! So regarding my original question, could I just merge the fasta files and follow that tutorial?
Comment: Expanding reference genome with alt loci and decoy sequences
by
Matthias Zepper
★
1.5k
Neither what ATpoint nor I wrote, contradicts this tutorial in any way. Furthermore, I trust, it is a good one when written by the GATK tea…
Comment: BLAST Database error: No alias or index file found for nucleotide database
by
Luke
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0
I had this error but fixed it by first "cd"-ing (changing directory) to the actual database-containing directory and *then* running the **b…
Answer: fgsea
by
LChart
▴
550
The gene list itself is permuted; so the comparison is the input ranking versus random rankings.
A phenotype permutation would be repeat…
Comment: Influence of ribosomal depletion efficiency on PCA clustering
by
LChart
▴
550
> I thought removing rRNA before normalization was a common practice, isn’t it that the case?
It is, and it's the right way to do it. My s…
Comment: Expanding reference genome with alt loci and decoy sequences
by
appropiate
▴
30
Thanks! I have replied to that recent comment since it has more participants. Please feel free to comment there as well!
Comment: Influence of ribosomal depletion efficiency on PCA clustering
by
Hugo
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20
Thanks for you answer.
As for your practical note, that indeed sounds wise, will definitely implement it.
On the other topic, I gave a tr…
Comment: Which hg38 file?
by
appropiate
▴
30
So would you not recommend [this tutoria][1]l as it is using GRCh38 with alternate contigs to map reads?
[1]: https://gatk.broadinstitu…
Answer: Correlation between two different datasets: between results of RNAseq and absenc
by
LChart
▴
550
CCA is an interesting idea; but one drawback is the binary nature of the effector matrix typically does not work that well with L2 objectiv…
Comment: Regarding filter primary alignment
by
bishopia
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0
nice. for the purposes of snp-calling, does it make sense to exclude not-properly-paired reads as well (e.g. add -f 0x02)?
Comment: List of cyanobacterial refseq genomes
by
Sam Wheeler
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0
Oh, that was easy, I feel so silly now. Thank you so, so much, you've really saved my life.
Comment: High proportion of non-biallelic SNPs in dbSNP 155 vs 144
by
Al Murphy
▴
30
Makes sense, would like to hear how your work progresses, I'm the creator of the [MungeSumstats R package](https://github.com/neurogenomics…
Answer: List of cyanobacterial refseq genomes
by
GenoMax
119k
Go to: https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=1117&annotated_only=true&refseq_annotation=true
Check the box marked below to s…
Answer: Expanding reference genome with alt loci and decoy sequences
by
Matthias Zepper
★
1.5k
Actually, your alignments will be worse when you expand a reference genome with alternate loci, see e.g. [this recent][1] comment by @atpoi…
Comment: High proportion of non-biallelic SNPs in dbSNP 155 vs 144
by
LChart
▴
550
Current: https://ftp.ncbi.nlm.nih.gov/snp/latest_release/VCF/
V151: https://ftp.ncbi.nlm.nih.gov/snp/pre_build152/organisms/human_9606_b15…
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