User: Paul

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Paul1.1k
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Posts by Paul

<prev • 150 results • page 1 of 15 • next >
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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 days ago by Paul1.1k
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Answer: A: Concatenating fastq.gz files across lanes
... If your FASTQ files have always suffix `*_L00*_R*_001.fastq.gz` , wich is standard Illumina output. This script should works - it concatenate fastq files according all lanes separate by R1 + R2: #!/bin/bash for i in $(find ./ -type f -name "*.fastq.gz" | while read F; do basename $F | ...
written 23 days ago by Paul1.1k
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Answer: A: confused about how to run pipeline
... Hi, first please create your access file (need to download exclude regions file): cnvkit.py access hg38.fa -x excludes.bed -o access-excludes.hg38.bed Then you can use batch command: cnvkit.py batch --target-avg-size 70 -p 12 TUMOR/*.bam --normal NORMAL/*.bam --targets capture_region.be ...
written 6 weeks ago by Paul1.1k
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Comment: C: How to replace row with another row in linux having NA and nucleotide bases
... if you are try to print first column - `awk '{print $1}' input` - does it work? When I test my on-liner on your pasted data above it is works. ...
written 12 weeks ago by Paul1.1k
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Comment: C: How to replace row with another row in linux having NA and nucleotide bases
... Hi, Are your files tab delimited? `cat -T input` is what result? ...
written 12 weeks ago by Paul1.1k
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Answer: A: How to replace row with another row in linux having NA and nucleotide bases
... you can use awk: cat file2 file1 | awk '!seen[$1,$2]++' | sort -k 1V,1 -k 2n,2 > result Output: A1 1 NA A1 2 NA A1 3 NA A1 4 A A1 5 C A1 6 T A1 7 NA A1 8 NA A1 9 NA A2 1 NA A2 2 NA A2 3 T A2 4 NA ...
written 12 weeks ago by Paul1.1k
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Answer: A: searching for genes included in the file name
... Or you can use `while` in bash. But if your files are big, this is not very fast solution. while read genes; do echo "----SEARCHING: $genes" grep -w "$genes" *.gene_ancestors.txt >> result done < gene_list.txt ...
written 12 weeks ago by Paul1.1k
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Comment: C: How can I find the same record in two file? Use python
... Hi, please can you use "code sample" when you paste code to your post? It is much more readable. ...
written 3 months ago by Paul1.1k
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Answer: A: benchmarking/validation tools for CNVs
... Hi, did you try [Ximmer][1] ?? It is "Ximmer is a tool designed to help users of exome and targeted genomic sequencing data accurately detect and interpret copy number variants (CNVs). Ximmer is not a copy number detection tool itself. Rather, it is a framework for running other copy number detectio ...
written 3 months ago by Paul1.1k
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Comment: C: Annovar annotation with refGene Database How to Dismiss Exon number and Gene Sym
... Hi, does it work for you? Can I change my comment to an answer? ...
written 3 months ago by Paul1.1k

Latest awards to Paul

Popular Question 10 days ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Popular Question 29 days ago, created a question with more than 1,000 views. For Compare my FASTA with Taxonomics group
Scholar 4 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Student 4 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Scholar 4 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Popular Question 4 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: For loop script
Student 7 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Appreciated 8 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Guru 8 months ago, received more than 100 upvotes.
Student 8 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Appreciated 8 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Compare two matrix
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For C: Is bcf just a bgzipped vcf?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Appreciated 9 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Scholar 9 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For Mask or trim primer sequences in Amplicon sequencing
Popular Question 10 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Student 10 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Popular Question 10 months ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Popular Question 11 months ago, created a question with more than 1,000 views. For How to compare assembly from Trinity and Velvet/Oases
Appreciated 12 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools

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