User: Paul

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Paul1.4k
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Posts by Paul

<prev • 161 results • page 1 of 17 • next >
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Comment: C: Calculate allele frequency from many VCF files in specific locus
... Yes `bcftools merge` is good idea. You can also use `GATK Combinegvcf`. bcftools query - (`bcftools query -f '%CHROM %POS[\t%DP\t%AD]\n'` ) gaves you DP and AD, and you would be able calculate frequencies. But frequency from all samples - just to get one number like in dbSNP. What about one genotyp ...
written 4 months ago by Paul1.4k
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Comment: C: Concatenating fastq.gz files across lanes
... What about to create link of fastq files or use output of find command? ...
written 6 months ago by Paul1.4k
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Answer: A: split vcf by individual
... Hi, another way is to use `bcftools` query and `GATK SelectVariants`. Code is here: cat split_vcf.sh Script looks: #!/bin/bash genome=~/path/to/reference/genome.fa for sample in `bcftools query -l INPUT.vcf`; do for i in *.vcf do gatk SelectVar ...
written 20 months ago by Paul1.4k
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Answer: A: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
... For very large BAM files (like WGS) I was tested Mosdepth [Link][1]. It is very fast and there are lot of option. Mosdepth can report the mean depth in 500-base windows genome-wide info under 9 minutes of user time with 3 threads. Example of syntax: mosdepth -n --fast-mode --by 500 sample.wgs ...
written 21 months ago by Paul1.4k
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Comment: C: Parser for Illumina Novaseq metadata
... Glad to help you (I was working on the same task last week :-))!!! ...
written 21 months ago by Paul1.4k
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Comment: C: Parser for Illumina Novaseq metadata
... Just fixed my typo in example - thanks. Yes those are shell command as alternative to parsing SAV data. ...
written 21 months ago by Paul1.4k
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Answer: A: Parser for Illumina Novaseq metadata
... Hi, look at the Illumina InterOP [Here][1]. You can use anaconda to install [here][2]. Syntax for data extraction is very easy and then you can plot data by gnuplot or R. example to get table (csv): interop_summary runfolder > /path/to/my/output example fot plotting: interop_plot_qs ...
written 21 months ago by Paul1.4k
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Answer: A: Bash scripting FastQC for multiple fastq files in multiple directories
... This could work: `find -maxdepth 5 -name "*fastq.gz" | parallel fastqc {} -o qc/` , then create easy script to move output to corresponding directory. ...
written 21 months ago by Paul1.4k
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Comment: C: speed up bcftools annotate command
... Hi, did you try GNU parallel? [Here][1] are some examples. I have good experiences to speed up all my processing tasks with parallel. [1]: https://gist.github.com/Brainiarc7/7af2ab5e88ef238da2d9f36b4be203c0 ...
written 21 months ago by Paul1.4k
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Answer: A: how to set metrics file when using MarkDuplicates in Picard
... Hi, my syntax looks like: picard -Xmx"$memory"g -Djava.io.tmpdir=$PWD/tmp -XX:ParallelGCThreads=$cpu MarkDuplicates I= ${p%.bam}.bam O= ${p%.bam}_rmdp.bam METRICS_FILE= ${p%.bam}_rmdp.txt CREATE_INDEX=true USE_JDK_DEFLATER=true USE_JDK_INFLATER=true Metrics should give you an statistics about ...
written 21 months ago by Paul1.4k

Latest awards to Paul

Appreciated 6 months ago, created a post with more than 5 votes. For A: Compare two matrix
Great Question 6 months ago, created a question with more than 5,000 views. For Does Illumina Undetermined Fastq files contain barcodes
Popular Question 9 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: For loop script
Popular Question 14 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Epic Question 15 months ago, created a question with more than 10,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 15 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For C: Is bcf just a bgzipped vcf?
Great Question 17 months ago, created a question with more than 5,000 views. For Extract specific reads from FASTQ files based on subsequence
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For C: Is bcf just a bgzipped vcf?
Epic Question 19 months ago, created a question with more than 10,000 views. For bash loop for alignment RNA-seq data
Popular Question 20 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Appreciated 20 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Great Question 21 months ago, created a question with more than 5,000 views. For Extract specific reads from FASTQ files based on subsequence
Scholar 21 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Scholar 21 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Popular Question 22 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Student 23 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Compare my FASTA with Taxonomics group
Scholar 2.5 years ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Student 2.5 years ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Scholar 2.5 years ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File

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