User: William

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William4.1k
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Posts by William

<prev • 305 results • page 1 of 31 • next >
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... Why is BBMAP more close to the sensitivity of BLAST than the other short read aligners like BWA/SNAP/minimap2? And is it still fast (since it is written in Java?)? ...
written 16 days ago by William4.1k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... Why is hisat2 more close to the sensitivity of BLAST than the other short read aligners like BWA/SNAP/minimap2? Is it because of the multiple index types? ...
written 16 days ago by William4.1k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... Correct, I am aligning DNA fragments of ca 200 bp against indexed genomes (DNA) of human size and smaller. ...
written 16 days ago by William4.1k
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Sensitive (BLAST like) and fast alignment of millions of sequences against human sized reference genomes
... Hi, What technology (both hardware & software) is out there that allows sensitive (BLAST like) and fast alignment of millions of sequences (c.a. 200bp) against multiple reference genomes? I know there is: - Normal software blast: Very sensitive but slow for many millions of sequences against ...
multicopy alignment lift over blast bwa written 16 days ago by William4.1k • updated 16 days ago by lieven.sterck600
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Comment: C: Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
... Gene model is mostly incomplete I think. ie. exons, transcripts and complete genes are missing. Also 2 predicted genes might actually be 1 gene. The gene models is based on 3rd party "push button analysis" ab initio + rna-seq based gene prediction (i.e. no manual curation, or consensus analysis of m ...
written 5 weeks ago by William4.1k
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Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
... **Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?** In the STAR RNA-seq aligner manual I read that a gene model should be used when indexing a reference genome before alignment. https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf > --sjdbGTFfile specie ...
gene_model incremental star rna-seq written 5 weeks ago by William4.1k • updated 5 weeks ago by Santosh Anand3.4k
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Comment: C: How to display a VCF/BCF file or stream as a paginated table in a python web fra
... Thanks I will have a look. Is thinks the correct link for xbrowse? https://github.com/macarthur-lab/seqr/tree/master/xbrowse ? It's wat google gives me and it is part of something called seqr. Do you have any additional documentation about xbrowse? And which stack is too slow for 100 samples? ...
written 4 months ago by William4.1k
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Comment: C: How to display a VCF/BCF file or stream as a paginated table in a python web fra
... I was thinking to use cyvcf2 to read the first 500 variants at the start of the file or the first 500 in a region of interest https://github.com/brentp/cyvcf2 . cyvcf2 can use the vcf.gz or bcf.csi index. From the cyvcf2 variant records I can create a simple table that I am looking to display using ...
written 4 months ago by William4.1k
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How to display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)?
... Does anyone know how display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)? Is this possible at all? The number of variants (i.e records) can be kept low trough pagination (e.g. 500). Number of samples (i.e. columns) might be several 100. I was thinki ...
vcf gui written 4 months ago by William4.1k
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How to do a local denovo assembly including unmapped paired reads for many samples to genotype a large insertion.
... I have a set of many bam files for which I would like to know if an insertion of a few 100bp is present at a certain locus. The insertion variant is not picked up by small variant callers like freebayes, gatk or structural variant callers like lumpy or manta when doing a full genome variant callin ...
local assembly written 6 months ago by William4.1k • updated 6 months ago by h.mon11k

Latest awards to William

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Where/How To Assess Which Bioinformatics Tools/Databases Are Most Used/Accessed?
Student 4 months ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
Student 4 months ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
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