User: roberto.spreafico

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1 month ago
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r****************@gmail.com

Posts by roberto.spreafico

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Viral de-novo Variant Call
... As a further comment, I think the main driver to choose between denovo assembly vs initial mapping followed by consensus is whether you start with a pure virus (in which case denovo assembly seems reasonable) or a mixture/non-clonal population (in which case denovo assembly might be messy, whereas m ...
written 6 months ago by roberto.spreafico20
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Comment: C: Viral de-novo Variant Call
... @Ribas I am quite interested in your approach. You are going thru the trouble of denovo assembly before variant calling to maximize mappability, correct? To a similar aim, I think another approach I have seen is to do a first round of mapping, generate a consensus sequence, and then remap to the con ...
written 6 months ago by roberto.spreafico20
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Comment: C: SNP-masking before short-read alignment to human genome
... Thanks Brian, pretty cool, I will give BBMap a try then! Thanks also for all your other suggestions, that is pretty useful! ...
written 4.9 years ago by roberto.spreafico20
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Comment: C: SNP-masking before short-read alignment to human genome
... Thank you Ashutosh, that is very clear and helpful! ...
written 4.9 years ago by roberto.spreafico20
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Comment: C: SNP-masking before short-read alignment to human genome
... Hi Ashutosh, what is your experience with Personal Genome Constructor? Do you see significant improvements over the standard human genome reference? ...
written 4.9 years ago by roberto.spreafico20
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Comment: C: SNP-masking before short-read alignment to human genome
... Thanks Brian! How does BBMap perform with spliced/split reads? Also, will higher sensitivity result in more multimappers that will be eventually discarded, or will precision remain high? Upon trimming reads, what min length do you suggest to retain to avoid reference bias? ...
written 4.9 years ago by roberto.spreafico20
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SNP-masking before short-read alignment to human genome
... Hello I was wondering if somebody has experience with aligning short reads to the reference human genome, and whether masking SNPs improves alignment and decreases reference bias. If masking is advised, how do you choose which SNPs to mask? Would dbSNP with MAF > 1% be a reasonable choice? Do yo ...
reference bias snp human rna-seq written 4.9 years ago by roberto.spreafico20 • updated 22 months ago by Biostar ♦♦ 20
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Comment: C: Reordering the bam file
... Thanks Devon, very clear. In my workflow I rehead a SAM file (with a bash script) to sort SQ header lines as I want. The product is still a SAM file. I then use picard to sort by coordinate (which now forces my SQ header line order) the SAM file, convert to BAM, and index, all together. This seems n ...
written 5.0 years ago by roberto.spreafico20
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Comment: C: Reordering the bam file
... I read this discussion with interest and wished you could clarify a point. Say that you generate an unsorted SAM file. When you invoke picard/samtools to sort by coordinate, the SQ header lines will be used to set how you reorder your reads. If you want a different order, it would make sense to me t ...
written 5.0 years ago by roberto.spreafico20 • updated 7 months ago by RamRS27k
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Matching Gencode annotations to Assemblies
... Hello, I am trying to match Gencode's annotations to assemblies. It is my understanding that the sequence of reference chromosomes changes only when there is a major version update (e.g. GRCh37 -> GRCh38). For minor versions (such as GRCh38.p2), patches (deltas between the major version and the ...
gtf assembly annotations gencode written 5.0 years ago by roberto.spreafico20 • updated 5.0 years ago by Emily_Ensembl20k

Latest awards to roberto.spreafico

Popular Question 4.8 years ago, created a question with more than 1,000 views. For Matching Gencode annotations to Assemblies
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Equivalence testing RNA-seq with edgeR
Popular Question 4.8 years ago, created a question with more than 1,000 views. For SNP-masking before short-read alignment to human genome

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