User: Paul

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Paul490
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490
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European Union
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3 years, 1 month ago
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Posts by Paul

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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 8 days 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 18 days 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 Isnt those regions "out of date" for HG38?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 19 days 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 19 days ago by Paul490 • updated 19 days ago by igor3.4k
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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 19 days 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 6 weeks ago by Paul490
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Comment: C: 16S rRNA seq software
... Thank you for moving to comment. I have overlook its rRNA. ...
written 6 weeks ago by Paul490
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Answer: A: What is the minimum coverage adequate for variant calls from Whole Genome Sequen
... In case you are calling germline variants - [this][1] is interesting article. Basically it is very hard to answer your question. Probably in exome sequencing it could be between 30x-50x. For WGS see [this][2] and [this] [3] interesting article. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PM ...
written 6 weeks ago by Paul490
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Comment: A: 16S rRNA seq software
... Look at the most recent rna-seq tools [here][1]. Maybe somebody have some additional own experiences. Best. [1]: https://omictools.com/rna-seq-category ...
written 6 weeks ago by Paul490
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Comment: C: how to extract particular regions of a sequence from fasta file if its range fo
... You are welcome. I tried it on the huge fasta file and it seems to me it works fast. Did my solution works? ...
written 6 weeks ago by Paul490

Latest awards to Paul

Centurion 8 days ago, created 100 posts.
Appreciated 12 days ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Great Question 4 weeks ago, created a question with more than 5,000 views. For bash loop for alignment RNA-seq data
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Appreciated 7 weeks ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Student 7 weeks ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 12 weeks 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 3 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
Student 4 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 5 months ago, created a question with more than 1,000 views. For Different coverage from bedtools and in vcf file - HELP PLEASE
Popular Question 5 months ago, created a question with more than 1,000 views. For Calculating GC content from BAM file by BED file
Popular Question 5 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Popular Question 11 months ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Student 12 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Student 13 months ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Popular Question 14 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 16 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
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Extract Information From Fastq Pair End Files
Popular Question 20 months ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
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Popular Question 22 months ago, created a question with more than 1,000 views. For Calculating GC content from BAM file by BED file
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For bash loop for alignment RNA-seq data
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