User: favero.francesco

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Posts by favero.francesco

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Ploidy vs. copy number in Sequenza
... Yes, when the normalised depth ratio is equal to 1, it means that the segment have copy number equal to the ploidy sample. It depends on the mechanism that have lead to the various rearrangements, but in a simple case, If ploidy is 3 it means that overall the chromosomes have 3 copies. In this case ...
written 2.6 years ago by favero.francesco120
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Comment: C: Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
... You can check with IGV if in the specific positions are present indels or other things that can justify the mismatch from depth and nucleotide counts. ...
written 2.9 years ago by favero.francesco120
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Answer: A: sequenza2PyClone bug in Sequenza
... Hi, I've seen this topic only now on Biostars :). The function is not exported in the namespace because I would not provide an "official" pyClone/sequenza integration, however the function is still accessible from the package: library(sequenza) sequenza:::sequenza2PyClone There is a post ...
written 2.9 years ago by favero.francesco120
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Comment: C: Extract Allele At Particular Positions From Bam Files
... I've recently suggested this on a similar post. Then you could check easily check the genotype. ...
written 5.2 years ago by favero.francesco120
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Answer: A: Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
... I wrote a tool to do exactly this; the function is called pileup2acgt, is written in python2.7 (compatible with the much faster pypy-2*). If you want to give it a try it works with no dependencies a part python2.7 core libraries. The tool is part of Sequenza, a program to detect copy number and var ...
written 5.2 years ago by favero.francesco120
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Answer: A: Hlacaller Gatk
... I've tried seq2HLA with illumina RNA-seq and, after some minor corrections on the code, it did work quite well. It gives you a resolution only on 2 digits though (eg HLA-A02). For this you need fastq files, that will be aligned to various HLA reference sequences with bowtie. I don't know if this is ...
written 5.2 years ago by favero.francesco120
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Answer: A: Anyone Has A Working Example On How To Run Broad'S Absolute On Exome Sequencing
... You don't need the MAF file to run ABSOLUTE, if you have the MAF it will be used with the detected copy number and cellularity to compute the cancer cell fraction of the mutations. Useful to infer sample heterogeneity. I found the current state of ABSOLUTE a bit lacking for exome, it does not prov ...
written 5.2 years ago by favero.francesco120

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Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Anyone Has A Working Example On How To Run Broad'S Absolute On Exome Sequencing
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Anyone Has A Working Example On How To Run Broad'S Absolute On Exome Sequencing

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