User: Stephane Plaisance

Reputation:
400
Status:
Trusted
Location:
Leuven area (Belgium)
Website:
http://users.ugent.be/...
Last seen:
2 weeks, 1 day ago
Joined:
8 years, 11 months ago
Email:
s*****************@gmail.com

molecular biologist slowly evolving towards data miner

Posts by Stephane Plaisance

<prev • 48 results • page 1 of 5 • next >
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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 7 months ago by Stephane Plaisance400
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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 7 months ago by Stephane Plaisance400
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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 7 months ago by Stephane Plaisance400
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sequencing to identify novel restriction sites
... I am looking for a sequencing protocol and associates tools to discover one or more consensus sites from DNA fragments digested by a novel enzyme. The template is plasmid sized and fully characterised, so I can map reads against it. The fragments range from 10's of bases to 100's and are quite ma ...
sequencing written 7 months ago by Stephane Plaisance400
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Comment: C: Download All The Bacterial Genomes From Ncbi
... 4) can be made faster with xargs and 8 parallel jobs like this: cat assembly_summary_complete_genomes.txt | xargs -I{} -n1 -P8 wget -P GbBac {}/*_genomic.fna.gz thanks @kristian for the very clear toturial! ...
written 9 months ago by Stephane Plaisance400
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Answer: A: bioawk output in original fastq format
... bioawk -c fastx '{print "@"$name" "$comment"\n"$seq"\n+\n"$qual}' input.fq > output.fq this should output a duplcate of the input, add more code to filter or modify any ...
written 9 months ago by Stephane Plaisance400 • updated 9 months ago by ATpoint21k
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Answer: A: look for the old version blast (not blast+)
... has moved to ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ for the latest version ...
written 12 months ago by Stephane Plaisance400
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Answer: A: Extracting Paired-End Reads Sitting In Different Chromosomes
... can be shortened to (including mapQ>5): samtools view -F 14 -q 5 -h input.sam \ | awk '$7 !~ /=/' \ | samtools view -Sb - \ > map_2_diff_chroms.bam ...
written 13 months ago by Stephane Plaisance400
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Comment: C: create a track with mismatch density from a SAM/bam file
... when I can compile this I will try (THANKS) ...
written 18 months ago by Stephane Plaisance400
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Answer: A: create a track with mismatch density from a SAM/bam file
... meanwhile rediscovered **bedtools bamtobed** which seems to do precisely what I want (-ed) when I can compile the java above, I will compare. S ...
written 18 months ago by Stephane Plaisance400

Latest awards to Stephane Plaisance

Commentator 3 months ago, created a comment with at least 3 up-votes. For A: Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
Popular Question 20 months ago, created a question with more than 1,000 views. For Change Span Size In Wig And Generate New File
Supporter 22 months ago, voted at least 25 times.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Ucsc Dbsnp131 Table Format
Great Question 2.9 years ago, created a question with more than 5,000 views. For Harvesting Known Disease Mutations
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Mitochondrial Haplogroup Determination
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Merging And De-Duplicating Structural Variant Calls (Bedpe)
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Change Span Size In Wig And Generate New File
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Change Span Size In Wig And Generate New File
Student 4.9 years ago, asked a question with at least 3 up-votes. For Mitochondrial Haplogroup Determination
Student 7.5 years ago, asked a question with at least 3 up-votes. For Mitochondrial Haplogroup Determination
Appreciated 7.9 years ago, created a post with more than 5 votes. For Harvesting Known Disease Mutations
Good Question 7.9 years ago, asked a question that was upvoted at least 5 times. For Harvesting Known Disease Mutations
Popular Question 7.9 years ago, created a question with more than 1,000 views. For Harvesting Known Disease Mutations
Student 7.9 years ago, asked a question with at least 3 up-votes. For Harvesting Known Disease Mutations
Teacher 9.0 years ago, created an answer with at least 3 up-votes. For A: Ucsc Dbsnp131 Table Format

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