User: Paul

gravatar for Paul
Paul600
Reputation:
600
Status:
Trusted
Location:
European Union
Last seen:
1 day, 9 hours ago
Joined:
3 years, 5 months ago
Email:
b********@gmail.com

about me

Posts by Paul

<prev • 110 results • page 1 of 11 • next >
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Comment: C: SNP data filtering from VCF file
... Hi, no Varscan is variant caller - it generates VCF from BAM file (mpileup). Did you tried [this][1] Pierre solution? [1]: https://www.biostars.org/p/7403/ ...
written 14 days ago by Paul600
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Comment: C: Compare two matrix
... Your are welcome. Sorry for bash solution - I am not familiar with perl. ...
written 14 days ago by Paul600
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Answer: A: Compare two matrix
... Hi, what about this bash solution: > paste -d '\n' matrix1 matrix2 | awk 'NR>1' | grep -v "\bP1\b" | awk '{if(! a[$1]){print; a[$1]++}}' CDS BC1-III BC1-IV BC10-II LOC105031928 175 181.5 99 LOC105031930 NA NA ...
written 15 days ago by Paul600
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Comment: C: SNP data filtering from VCF file
... Hi, what variant caller do you use? Some of them have an option to call INDELS and SNP separately - for example VarScan.. ...
written 15 days ago by Paul600
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... So you prefer to hard trim FASTQ files from primer sequences instead of soft clipping in BAM? ...
written 6 weeks ago by Paul600
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Answer: A: Best Copy Number Variation Tools
... Hi, I have very good experiences with CNVkit - this is very robust tool and works perfectly fine for Capture enrichment library (also author mention good results for WGS and Amplicon panels, but did not validate). We are right now validating this tool and looks perfectly fine. This tool is very fast ...
written 8 weeks ago by Paul600
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Comment: C: Convert Refseq Id To Gene Name
... Hi, I am not perl person - would be possible to change this script to paste LIST of NM_numbers instead of typing to STDIN in cmd?? ...
written 3 months ago by Paul600
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Comment: C: gVCF questions with "0" in the Alt field
... Please edit your original question and do not post additional information as an answer. ...
written 3 months ago by Paul600
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Comment: C: gVCF questions with "0" in the Alt field
... Does not it mean, that alternative allele depth is zero? So it is mean, that you have only reference (ref) allele count? Can you copy/paste part of your gVCF? ...
written 3 months ago by Paul600
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How to interpret tandem SNP in
... Dear all, does anybody have experiences with this examle in variant calling: Lets assume reference is: AAA**CGT**AAA And its aligned reads is: AAA**GGC**AAA My output from VarScan is: 4C>G 6T>C But some algorithms detected variants like: delCGTinsGGC Finally th ...
varscan ngs dna-seq variants written 3 months ago by Paul600

Latest awards to Paul

Appreciated 13 days ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Scholar 13 days ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Student 13 days ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Popular Question 26 days ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Appreciated 5 weeks ago, created a post with more than 5 votes. For bash loop for alignment RNA-seq data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Great Question 3 months ago, created a question with more than 5,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 4 months ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Centurion 4 months ago, created 100 posts.
Appreciated 4 months ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Great Question 5 months ago, created a question with more than 5,000 views. For bash loop for alignment RNA-seq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Appreciated 5 months ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Student 5 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 6 months ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Popular Question 7 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
Student 9 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 9 months ago, created a question with more than 1,000 views. For Different coverage from bedtools and in vcf file - HELP PLEASE
Popular Question 9 months ago, created a question with more than 1,000 views. 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 Filter out specific reads from FASTQ files
Popular Question 15 months ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Student 17 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Student 17 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file

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