Moderator: lieven.sterck

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lieven.sterck6.9k
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VIB, Ghent, Belgium
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Posts by lieven.sterck

<prev • 1,375 results • page 1 of 138 • next >
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Comment: C: understanding CD hit command
... Have you tried looking into the manual/help pages of the CDHIT software? ...
written 1 day ago by lieven.sterck6.9k
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Comment: C: makeblastdb with fasta error: BLAST options error
... noted, thx for looking into it https://www.biostars.org/u/55/ curious to hear what the NCBI blast team has to say for it ;) ...
written 1 day ago by lieven.sterck6.9k
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Comment: C: makeblastdb with fasta error: BLAST options error
... if you don't really need it (though I would personally also always add it ) you could avoid this behaviour by omitting the `-parse_seqids` parameter but this is definitely a patch approach rather than a solid solution ...
written 1 day ago by lieven.sterck6.9k
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Answer: A: Subsetting GFF3 files for gene models using Bash
... if you consider awk as being bash enough, this little bash script should work: for i in `cat ` do base=${i%.*} awk -v base="=$base;" -v name="=$i;" '($3 == "gene" && $9 ~ base) || $9 ~ name' done this takes as input your original geneID list (so the full name) and r ...
written 1 day ago by lieven.sterck6.9k
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Answer: A: location of integrated vector in the genome in CRISPR experiment
... The approach offered by https://www.biostars.org/u/14684/ in this post https://www.biostars.org/p/225399/ has proven its value and efficiency several times for me when identifying Tdna insertion sites (I'm assuming it would work as well for CRISPR insertions). The only requisite is that you know th ...
written 1 day ago by lieven.sterck6.9k
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Comment: C: location of integrated vector in the genome in CRISPR experiment
... what kind of data do you have? your question is very brief, Please go through https://www.biostars.org/p/357878/ and then consider editing your question. ...
written 1 day ago by lieven.sterck6.9k
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... yes it is, but as https://www.biostars.org/u/30/ and https://www.biostars.org/u/25721/ pointed out, it's more future-proof if you go for one of the pipeline manager tools ...
written 2 days ago by lieven.sterck6.9k
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Comment: C: Msc in bioinformatics recommendation
... I know of one at Ghent University, but that does not offer the month study - month work option though. It does offer the possibility to do some internship/project in a company (of choice) ...
written 2 days ago by lieven.sterck6.9k
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Comment: C: Promals is not taking the accurate name of FASTA sequence
... Is it correct that there are no '`>`' chars (to denote the sequence headers?). Is this supposed to be a fasta file? ...
written 2 days ago by lieven.sterck6.9k
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... looks like it does not get the `$outputDir` correctly. and as such tries to write to the root folder / to which you might not have access can you post all output from your script (and perhaps add an `echo $outputDir` in it) ...
written 2 days ago by lieven.sterck6.9k

Latest awards to lieven.sterck

Scholar 6 days ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 27 days ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 5 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 9 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 10 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 8 months ago, created an answer that has been accepted. For A: List of all GO terms
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Delete numbers in the tables column
Scholar 8 months ago, created an answer that has been accepted. For A: List of all GO terms
Appreciated 8 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header

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