User: Paul

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Paul490
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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 17 days ago by Paul490
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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 18 days ago by Paul490
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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 21 days ago by Paul490
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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 22 days ago by Paul490
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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 5 weeks ago by Paul490
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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 6 weeks ago by Paul490
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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 Isnt those regions "out of date" for HG38?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 6 weeks ago by Paul490
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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 6 weeks ago by Paul490 • updated 6 weeks ago by igor3.6k
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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 6 weeks ago by Paul490
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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 10 weeks ago by Paul490

Latest awards to Paul

Great Question 11 days ago, created a question with more than 5,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 29 days ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Centurion 5 weeks ago, created 100 posts.
Appreciated 5 weeks ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Great Question 8 weeks ago, created a question with more than 5,000 views. For bash loop for alignment RNA-seq data
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Appreciated 11 weeks ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Student 11 weeks ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 3 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 4 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
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 Different coverage from bedtools and in vcf file - HELP PLEASE
Popular Question 6 months ago, created a question with more than 1,000 views. For Calculating GC content from BAM file by BED file
Popular Question 6 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
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Popular Question 15 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 17 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Popular Question 19 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
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