User: Gabriel R.

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Gabriel R.2.5k
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Location:
Center for Geogenetik Københavns Universitet
Website:
https://grenaud.github...
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gabrielylr
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5 hours ago
Joined:
6 years, 8 months ago
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m***************@yahoo.com

Now postdoc at the Center for Geogenetics at Copenhagen University. In a former life, I was a Ph.D student in bioinformatics at the Max Planck Institute for Evolutionary Anthropology/ Interested in sequencing, particularly ancient DNA and inference of demography. 

Posts by Gabriel R.

<prev • 335 results • page 1 of 34 • next >
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Answer: A: Demultiplexing before merging paired-end reads?
... This post is between a comment and a response. I work a lot with ancient DNA where fragments are very short (e.g. 40bp). This entails that even for a paired-end run you constantly have to deal with "single-end" reads (merged paired-end) and genuine paired-end data. The logic was getting very convolu ...
written 25 days ago by Gabriel R.2.5k
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Comment: C: reference genome hs37d5 with PhiX
... I am no longer there, I will ask my former supervisor, let's see if they can stick it somewhere. in the meantime, here are the accessions for the reference: http://cdna.eva.mpg.de/neandertal/Chagyrskaya/bam/README ...
written 10 weeks ago by Gabriel R.2.5k
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Comment: C: reference genome hs37d5 with PhiX
... perhaps I am wrong but there is no "the reference with PhiX". When I was at the Max Planck Inst. in Leipzig, we made our own by concatenating the human reference and some decoy sequences. I suggest you contact the center in question that produced the BAM file. ...
written 10 weeks ago by Gabriel R.2.5k
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Answer: A: deML 'rgqual' parameter
... The rgqual refers to the Z_0 score. Z_0 is the likelihood for the top (most likely) read group on a PHRED scale. Considering the sequence of this read group as the template to sequence and using the principle of independence between bases, this likelihood is computed as: Z_0= -10 * log_10{ PROD ...
written 10 weeks ago by Gabriel R.2.5k
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Comment: C: Calculate average mapping quality at a position
... it depends on the aligner but it in any case, it's a bit of a scam: https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/ The link above has a plot of the distribution of mapping qualities. ...
written 4 months ago by Gabriel R.2.5k
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Comment: C: Calculate average mapping quality at a position
... I think this is using "samtools mpileup -s" which outputs the base quality followed by the mapping qualities for the read that supports the base. ...
written 4 months ago by Gabriel R.2.5k
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Answer: A: Calculate average mapping quality at a position
... These are probabilities of mismapping on a PHRED scale. For the first one, the probability of mismapping is: (10^(-(39/10)) = 0.0001258925 For the second it is: 10^(-(50/10)) = 1e-05 So on average, your probability of mismapping is: (0.0001258925+1e-05)/2 = 6.794627e-05 On a PHRE ...
written 4 months ago by Gabriel R.2.5k
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Comment: C: TCGA SNP to plink
... Could you send a direct link to the MAF file you want to convert? ...
written 4 months ago by Gabriel R.2.5k
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Comment: C: Convert beagle output file to plink
... I just saw, this can you please provide a link to the format that you have? ...
written 5 months ago by Gabriel R.2.5k
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Comment: C: samtools and I/O redirection
... let's take a step back, why do you want a sam file to begin with? ...
written 5 months ago by Gabriel R.2.5k

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Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
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Popular Question 28 days ago, created a question with more than 1,000 views. For Psmc Parameters To Use
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
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Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
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