User: Stephane Plaisance

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410
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Location:
Leuven area (Belgium)
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http://users.ugent.be/...
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1 day, 4 hours ago
Joined:
9 years, 10 months ago
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molecular biologist slowly evolving towards data miner

Posts by Stephane Plaisance

<prev • 55 results • page 1 of 6 • next >
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Comment: A: bcftools filtering on INFO fields
... One of these bad days, I used -e (exclude) instead of -i (include) Sorry about this! It now works (of course) ...
written 15 days ago by Stephane Plaisance410
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Comment: A: bcftools filtering on INFO fields
... You are right, only '/' is valid but does not work for me Should the VCF be bgzipped and indexed or does this normally work on plain text? ...
written 15 days ago by Stephane Plaisance410
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bcftools filtering on INFO fields
... below is a piece of my VCF where I try to extract rows with SUPPORT>10 but fail to specify such filter. I tried: `bcftools filter -sFilterName -e 'INFO/SUPPORT>10' variants.vcf` (typo edited) result is no filtering with all the input going through I do not find a page with working examples b ...
vcf bcftools variant variants written 15 days ago by Stephane Plaisance410
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Answer: A: Count Of Variants
... if you want a fancy output, here is a development based on the top answer above with some gawk magic cat \ | vcf-annotate --fill-type \ | grep -v '^#' \ | gawk ' BEGIN{ FS="\t"; OFS="\t" } { match($8, /TYPE=([^ ]+)/, arr); type=arr[1]; le ...
written 16 days ago by Stephane Plaisance410
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Comment: C: adding suffix /1 & /2 to PE data - abyss input data
... did not work for me because the names were of the type > @HISEQ:149:C76YNACXX:3:1101:1159:2191 1:N:0:GCCAAT and MBBMap added the /1 to look like this > @HISEQ:149:C76YNACXX:3:1101:1159:2191 1:N:0:GCCAAT /1 instead of producing > @HISEQ:149:C76YNACXX:3:1101:1159:2191/1 for me, the solu ...
written 29 days ago by Stephane Plaisance410
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how to best rotate a chloroplast plastid map
... I would like to produce a series of Pt.DNA maps for different plants and would like to represent them correctly. I will be using GeSeq and OGDraw (https://chlorobox.mpimp-golm.mpg.de/) Now, is there a best practice on where to position the +1 of a circular plastid genome and how to orientate the map ...
assembly plastid written 4 weeks ago by Stephane Plaisance410
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SNPEFF genome build with specific codon usage
... Failing to build my own Arabidopsis thaliana reference with Mt using 'codon.Mitochondrial' and Pt using 'codon.Bacterial_and_Plant_Plastid' but the same commands works well with both lines with codon tables removed below. The snpeff commands java -Xms24g -Xmx24g -jar /opt/biotools/snpEff/snpE ...
annotation snpeff variants written 12 weeks ago by Stephane Plaisance410 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: sequencing to identify novel restriction sites
... same comment as above but you are right, short reads should be good enough. Thanks lieven ;-) ...
written 18 months ago by Stephane Plaisance410
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Comment: C: sequencing to identify novel restriction sites
... It is close indeed but RAD seq implies (as far as I understand it) further fragmentations and in our case we already have a majority of fragments smaller than 100bps. Therefore I think we will need to tag the ends somehow and make concatemers to be amendable to sequencing which otherwise would disc ...
written 18 months ago by Stephane Plaisance410
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Comment: A: sequencing to identify novel restriction sites
... I am looking for a sequencing method to identify the restriction sites from processed template and derive consensus sequence(s) specific for that nuclease. ...
written 18 months ago by Stephane Plaisance410

Latest awards to Stephane Plaisance

Popular Question 10 months ago, created a question with more than 1,000 views. For Merging And De-Duplicating Structural Variant Calls (Bedpe)
Commentator 14 months ago, created a comment with at least 3 up-votes. For A: Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Change Span Size In Wig And Generate New File
Supporter 2.8 years ago, voted at least 25 times.
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Ucsc Dbsnp131 Table Format
Great Question 3.8 years ago, created a question with more than 5,000 views. For Harvesting Known Disease Mutations
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Mitochondrial Haplogroup Determination
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Merging And De-Duplicating Structural Variant Calls (Bedpe)
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Change Span Size In Wig And Generate New File
Student 5.8 years ago, asked a question with at least 3 up-votes. For Mitochondrial Haplogroup Determination
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Change Span Size In Wig And Generate New File
Student 8.4 years ago, asked a question with at least 3 up-votes. For Mitochondrial Haplogroup Determination
Popular Question 8.8 years ago, created a question with more than 1,000 views. For Harvesting Known Disease Mutations
Student 8.8 years ago, asked a question with at least 3 up-votes. For Harvesting Known Disease Mutations
Appreciated 8.8 years ago, created a post with more than 5 votes. For Harvesting Known Disease Mutations
Good Question 8.8 years ago, asked a question that was upvoted at least 5 times. For Harvesting Known Disease Mutations
Teacher 9.9 years ago, created an answer with at least 3 up-votes. For A: Ucsc Dbsnp131 Table Format

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