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Recent Replies
Answer: Expanding reference genome with alt loci and decoy sequences
by
Matthias Zepper
★
1.4k
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
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480
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…
Comment: Why isn't GWAS used in oncology?
by
LChart
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480
This is a definitional issue. If you define a GWAS as [looking specifically at inherited mutations][1], then associations of tumor mutation…
Answer: Plink : Variant names are limited to 16000 characters
by
chrchang523
9.5k
You want to use `--new-id-max-allele-len 50 missing` with --set-all-var-ids or --set-missing-var-ids; '[missing][1]' specifies that when a …
Comment: Loading a pre-filtered loom file into pySCENIC
by
Jacob
•
0
the file has a loom1 extension, is that the problem? the loom file is able to be read by sc.read_loom.
Comment: High proportion of non-biallelic SNPs in dbSNP 155 vs 144
by
chrchang523
9.5k
Suppose the human population is ~80% A, ~20% G, and ~0.001% T at a SNP. It's quite likely that we'd only have confident observations of A/…
Comment: Why do I have sequential 100 G (GGGGGGGGGG...) in R2 FastQC report?
by
rpolicastro
9.4k
That's still a large percentage, so it may be worth talking to the sequencing provider.
Comment: Why do I have sequential 100 G (GGGGGGGGGG...) in R2 FastQC report?
by
Giulia.cosenza
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70
No, not every R2, you can see the % in the picture I posted
Comment: Gene Set Enrichment Analysis
by
ATpoint
64k
Basically you would need to replace the differential analysis part with something that accepts normalized data. That could be the limma-tre…
Comment: Gene Set Enrichment Analysis
by
Aadil Rashid
•
0
Sorry if it sounds naive of me but how to make this tutorial work for normalized sequence data?
Comment: How to get results from a curl
by
Matthias Zepper
★
1.4k
Your code currently returns:
response.json()
{'jobId': 'db942c3c2818e24dc10010136c59c89c2acdef7e'}
I have no idea, how this API w…
Comment: DEXSeq Error loading in data set - subscript out of bound
by
osiemen
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20
Indeed thats what I had to do as well!
Answer: DEXSeq Error loading in data set - subscript out of bound
by
uwe.schwartz
▴
10
Had the same problem. Removing the quotes from the count table did the job.
Comment: transcription binding site prediction from fasta sequence
by
ATpoint
64k
There is now also a wrapper package for the MEME suite (that includes FIMO) in R/Bioconductor: https://bioconductor.org/packages/release/bi…
Answer: transcription binding site prediction from fasta sequence
by
rpolicastro
9.4k
JASPAR allows exporting motifs in MEME format which you can use along with [FIMO](https://meme-suite.org/meme/tools/fimo) from the MEME sui…
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