User: Phil Ewels

gravatar for Phil Ewels
Phil Ewels70
Reputation:
70
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Location:
Sweden / Stockholm / SciLifeLab
Website:
http://phil.ewels.co.uk/
Twitter:
tallphil
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Last seen:
1 week, 4 days ago
Joined:
2 years, 11 months ago
Email:
p*********@scilifelab.se

Bioinformatician working for the NGI Applications group at SciLifeLab in Stockholm. Interested in epigenetics. Author of MultiQC.

Posts by Phil Ewels

<prev • 17 results • page 1 of 2 • next >
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Comment: C: How to calculate the percent of methylated cytosines.
... If you post a link to the paper that would help to clarify the question :) ...
written 11 days ago by Phil Ewels70
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Comment: C: How to calculate the percent of methylated cytosines.
... If you want for all Cytosines, not context specific (CpG / CHG / CHH as printed in the report) just add the numbers: * Total C's analysed `1218062196` * Methylated C's in CpG context `31593318` * Methylated C's in CHG context `1525159` * Methylated C's in CHH context `3319601` ``` ( (31593318 + 15 ...
written 12 days ago by Phil Ewels70
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Answer: A: How to calculate the percent of methylated cytosines.
... Tools such as [Bismark](https://www.bioinformatics.babraham.ac.uk/projects/bismark/) and [bwa-meth](https://github.com/brentp/bwa-meth) align WGBS reads and then extract the methylation status of every cytosine within each aligned read. They also produce summary statistics, including the genome-wide ...
written 12 days ago by Phil Ewels70
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Comment: C: Too low mapping percentage using HISAT2 on human reference genome.
... RNA-seq data has reads that span exon-exon boundaries. BowTie will not align these reads, so you'll only get back alignments that lie entirely within an exon. Tophat / STAR etc are "splice aware" aligners, so work with RNA-seq data. ...
written 12 days ago by Phil Ewels70
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Comment: C: Too low mapping percentage using HISAT2 on human reference genome.
... Ouch! Maybe time to start running [FastQ Screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) routinely.. :) ...
written 13 days ago by Phil Ewels70
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Comment: C: Too low mapping percentage using HISAT2 on human reference genome.
... Ah yes, absolutely. I guess it depends on how extreme the base composition wobbling is.. I was imagining 100% for each base but on re-reading the OP it could well be hexamer priming as you say. ...
written 13 days ago by Phil Ewels70
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Comment: C: Too low mapping percentage using HISAT2 on human reference genome.
... Whilst I agree that contamination with another species is a concern, I can't see how this would affect the base composition for the first 10 bp of each read? ...
written 13 days ago by Phil Ewels70
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Answer: A: Are all antisense transcripts from polyA enriched library RNA-seq polyadenylated
... One possible explanation for this is a poor efficiency of the poly-A enrichment, possibly combined with DNA contamination. No enrichment is ever 100% efficient, so other material can always get into the library. If you have antisense reads in exons, this can sometimes be due to DNA contamination. Th ...
written 13 days ago by Phil Ewels70
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Comment: C: Too low mapping percentage using HISAT2 on human reference genome.
... It's probably worth trying the 5' trimming approach from my answer below first.. ;) I'm pretty sure that'll fix your problems and it's not to do with your reference. ...
written 14 days ago by Phil Ewels70
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Comment: C: Too low mapping percentage using HISAT2 on human reference genome.
... I would be very surprised if this has much effect on your alignments. These extra scaffolds are recommended to "soak up" reads which would otherwise misalign, but they shouldn't account for more than a few of % of your library. That can be a problem for downstream analysis, but won't result in a glo ...
written 14 days ago by Phil Ewels70

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