User: Paul

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Paul500
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European Union
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3 years, 3 months ago
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Posts by Paul

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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 7 weeks ago by Paul500
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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 7 weeks ago by Paul500
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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 8 weeks ago by Paul500
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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 8 weeks ago by Paul500
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... Does it make a sense to trim each amplicom -30 bp separately for forward and reverse orientation? ...
written 10 weeks ago by Paul500
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Comment: C: known unmappable or poorly sequenced regions in hg38
... Thank you Igor. Did you validate this regions? I can see, that for build GRCh38 is there only 38 regions. For Hg19 it is 411 regions. Also when I check [this][1] version of BED, there are 1649 regions. [1]: ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/ ...
written 11 weeks ago by Paul500
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Comment: C: known unmappable or poorly sequenced regions in hg38
... Thank you so much. I was thinking to use "wgEncodeDukeMapabilityRegionsExcludable.bed.gz" from [here][1] and then use UCSC liftOver, but is this good procedure? Isnt those regions "out of date" for HG38? [1]: ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/ ...
written 11 weeks ago by Paul500
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known unmappable or poorly sequenced regions in hg38
... Dear all, is there any similar file to [this][1], which known unmappable or poorly sequenced regions for hg38? Or any way to download it from ucsc table browser? Thank you for any link or comments. [1]: ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/ ...
bed ngs dna-seq written 11 weeks ago by Paul500 • updated 11 weeks ago by igor3.9k
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Answer: A: converting multiple bed files to equivalent intervals
... Hey, try to use [CNVkit][1] tool - there is an option `--split` in `target` argument: cnvkit.py target my_baits.bed --split -o my_targets.bed cnvkit.py target -h --split Split large tiled intervals into smaller, consecutive targets. ...
written 11 weeks ago by Paul500
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Comment: C: Varscan Filters Not Being Applied
... Any update? I have the same issue and it is over 3 years later old post.. ...
written 3 months ago by Paul500

Latest awards to Paul

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Great Question 6 weeks ago, created a question with more than 5,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 9 weeks ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Centurion 10 weeks ago, created 100 posts.
Appreciated 10 weeks ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Great Question 3 months ago, created a question with more than 5,000 views. For bash loop for alignment RNA-seq data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Appreciated 3 months ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Student 3 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
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...
Popular Question 5 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
Student 7 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 7 months ago, created a question with more than 1,000 views. For Different coverage from bedtools and in vcf file - HELP PLEASE
Popular Question 7 months ago, created a question with more than 1,000 views. For Calculating GC content from BAM file by BED file
Popular Question 8 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
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Student 15 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Student 15 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Popular Question 16 months ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Popular Question 21 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
Popular Question 21 months ago, created a question with more than 1,000 views. For How To Extract Information From Fastq Pair End Files
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