User: William

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William4.7k
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Posts by William

<prev • 339 results • page 1 of 34 • next >
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Comment: C: How to convert a VCF with genotypes and phasing info to list of haplotypes for R
... I have Illumina 150bp sequencing data for multiple samples. I am looking to leverage the phase information from the sequencing data to determine the haplotypes for small regions of interest. Regions can be as small as 100bp, or 150, so even within the Illumina read length. ...
written 6 days ago by William4.7k
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How to convert a VCF with genotypes and phasing info to list of haplotypes for ROI/SOI
... How to convert a VCF with genotypes and phasing info to list of haplotypes for ROI/SOI? VCF files created with GATK HaplotypeCaller/GenotypeGVCFs include genotypes and the phase between close by heterozygous genotypes. In theory this should make it possible to output haplotypes for a Region Of In ...
vcf haplotypes genotypes phasing written 6 days ago by William4.7k • updated 6 days ago by 4galaxy7790
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Comment: C: How to filter a gff3 file by gene IDs
... I could use this agat script from the latest agat version for the filtering. ...
written 16 days ago by William4.7k
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Comment: C: How to filter a gff3 file by gene IDs
... Thank you. I'll install a recent version of AGAT and then try this. ...
written 22 days ago by William4.7k
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Comment: C: How to filter a gff3 file by gene IDs
... I looked at the AGAT documentation. But I could not find a AGAT command that could do this filtering. Can you share which command to use, with which options. Thank you. ...
written 23 days ago by William4.7k
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How to filter a gff3 file by gene IDs
... How to filter a gff3 file by gene IDs? Just grepping on the IDs does output the exons and other features that are below the gene. I thought this would be a common use case. But can't find a command line tool that can filter a gff3 file based on IDs provided on the CLI or in a file. ...
gff3 written 27 days ago by William4.7k
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Answer: A: How to "discover" read structure and barcodes given Illumina sequencing run dire
... Just convert the entire sequences to fastq without de-multiplexing and without trimming. Note that you need to set the entire read length to template. **148T** in this example. picard IlluminaBasecallsToFastq B=./{MY_RUN}/Data/Intensities/BaseCalls/ L=1 RS=148T INCLUDE_NON_PF_READS=false ...
written 29 days ago by William4.7k
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How to "discover" read structure and barcodes given Illumina sequencing run directory
... Is there any tool to discover the read structure and barcodes used in a random Illumina sequencing run directory? I have some Illumina sequencing run directories where I don't have all the information needed to demultiplex the run. With Illumina sequencing run I mean a directory like Data/Intens ...
illumina bcl barcodes demultiplexing written 4 weeks ago by William4.7k • updated 29 days ago by GenoMax94k
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Comment: C: Count all (non N) nucleotides within regions defined in BED file
... Thank you. I'll use the pyfastx fasta composition to compare the content of the getfasta and original fasta file. Also added that option to the linked question. ...
written 7 weeks ago by William4.7k
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Answer: A: Counting base and nucleotide frequency of multifasta file
... pyfastx can also get the base composition of a fasta file. https://pypi.org/project/pyfastx/ import pyfastx fa = pyfastx.Fasta('test/data/test.fa.gz') fa.composition {'A': 24534, 'C': 18694, 'G': 18855, 'T': 24179} ...
written 7 weeks ago by William4.7k

Latest awards to William

Scholar 29 days ago, created an answer that has been accepted. For A: bcftools filter applied to specific sample column
Teacher 7 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?
Great Question 7 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Great Question 8 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Best Copy Number Variation Tools
Scholar 8 months ago, created an answer that has been accepted. For A: bcftools filter applied to specific sample column
Great Question 8 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Teacher 11 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?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Multi-Sample Vcf To Phylogenetic Tree.
Appreciated 11 months ago, created a post with more than 5 votes. For A: Best Genome Browser To Look At Structural Variation Calls
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Popular Question 15 months ago, created a question with more than 1,000 views. For Google Genomics and Broad Institute Team Up to Tackle Genomic Data
Great Question 15 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Great Question 21 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Appreciated 21 months ago, created a post with more than 5 votes. For A: Best Genome Browser To Look At Structural Variation Calls

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