User: Paul

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Paul1.3k
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Posts by Paul

<prev • 159 results • page 1 of 16 • next >
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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 11 months ago by Paul1.3k
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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 12 months ago by Paul1.3k
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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 12 months ago by Paul1.3k
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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 12 months ago by Paul1.3k
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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 12 months ago by Paul1.3k
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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 13 months ago by Paul1.3k
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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 13 months ago by Paul1.3k
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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 13 months ago by Paul1.3k
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Answer: A: How to convert NGS .tabular file to excel file?
... Hi, here is an python script which takes as first argument TSV and second argument creates xlsx file. import csv import sys reload(sys) sys.setdefaultencoding('utf8') from xlsxwriter.workbook import Workbook # Add some command-line logic to read the file names. tsv ...
written 14 months ago by Paul1.3k
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Comment: C: Parsing Blast output on linux/unix
... Did you try install [bioperl][1] to your system?? Bio::SearchIO is module of Bioperl. [1]: https://bioperl.org/INSTALL.html ...
written 17 months ago by Paul1.3k

Latest awards to Paul

Popular Question 27 days ago, created a question with more than 1,000 views. For How to show whole blast contig
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: For loop script
Popular Question 5 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Epic Question 6 months ago, created a question with more than 10,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 7 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For C: Is bcf just a bgzipped vcf?
Great Question 9 months ago, created a question with more than 5,000 views. For Extract specific reads from FASTQ files based on subsequence
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For C: Is bcf just a bgzipped vcf?
Epic Question 11 months ago, created a question with more than 10,000 views. For bash loop for alignment RNA-seq data
Popular Question 11 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Appreciated 12 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Great Question 12 months ago, created a question with more than 5,000 views. For Extract specific reads from FASTQ files based on subsequence
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Scholar 12 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Scholar 13 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Popular Question 14 months ago, created a question with more than 1,000 views. For How to show whole blast contig
Student 14 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 17 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Popular Question 18 months ago, created a question with more than 1,000 views. For Compare my FASTA with Taxonomics group
Scholar 21 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Student 21 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
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 Filter out specific reads from FASTQ files
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: For loop script

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