Moderator: lieven.sterck

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lieven.sterck9.5k
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VIB, Ghent, Belgium
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still need to add some info here

Posts by lieven.sterck

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Answer: A: Can someone kindly explain upstream vs. downstream?
... if a protein catalyses a certain reaction (A) and the resulting compound serves as input for another reaction in a different pathway (B) you denote it as downstream of the pathway where this first protein (or reaction) is part of. Pathway B needs pathway A to function, it is thus downstream in the c ...
written 20 hours ago by lieven.sterck9.5k
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Comment: C: When a duplicated BUSCOs value is too high? Reasons and how to improve it
... well yes and no :) have a look at the details how those BUSCO groups are build. If I remember correctly they need to be single copy in at least x% of the species under investigation. If you would be very stringent (== single copy in all species) you'll end up with only a few dozens to hundreds (we ...
written 20 hours ago by lieven.sterck9.5k
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Answer: A: When a duplicated BUSCOs value is too high? Reasons and how to improve it
... Without knowing the details I would say, no, that's not too high, nor a worrying result. It's very well known that in plants you often have a substantial amount of duplicated genes, and 10% is not high in that respect. If there is some redundancy in your assembly that can also increase the amount o ...
written 1 day ago by lieven.sterck9.5k
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Comment: C: Error in Blast+
... check the memory usage. This error might be linked to the memory usage? what are the specs of your machines (or resources assigned to this job)? ...
written 3 days ago by lieven.sterck9.5k
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Comment: C: How to merge two gff3 files?
... depends on what exactly you want to achieve but yes, `agat_sp_merge_annotations.pl` sounds about right. alternatively you can first cat both gff files together and then run `agat_convert_sp_gxf2gxf.pl` to fix the 'issues' . On their github page there are lots of explanations and guidelines on wha ...
written 4 days ago by lieven.sterck9.5k
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Answer: A: How to merge two gff3 files?
... I use [AGAT][1] for that and many other GFF processing things as well. https://www.biostars.org/p/413510/ [1]: https://github.com/NBISweden/AGAT ...
written 4 days ago by lieven.sterck9.5k
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Comment: C: Extract the overlapping paired-end reads
... not directly what you ask for but you could first merge overlapping reads (eg with `FLASH` or `BBMerge` or such) and then map those and see where they map. ...
written 5 days ago by lieven.sterck9.5k
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Comment: C: Merging multiple tsv files
... if you need to merged them (column-wise , we don't have enough info to figure that out), have a look at the linux `paste` command ...
written 5 days ago by lieven.sterck9.5k
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Comment: C: Blast + Alignement Shell Script
... Not saying that this BIRCH interface might not have its merits but most often if you want to write a bash script it's to automated a process to be run in batch, quite the opposite as what a GUI offers, no? Does BIRCH comes with its own versions of blast or other software or does those have to be av ...
written 6 days ago by lieven.sterck9.5k
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Comment: C: Blast + Alignement Shell Script
... there is very little info to work on here, eg. what does the `$1` `$2` ... stand for? I also noticed you have twice `$3` but in different places that do not make sense to have the same input. for extracting sequences based on a blast result you better use `blastdbcmd` from the blast package, as inp ...
written 6 days ago by lieven.sterck9.5k

Latest awards to lieven.sterck

Scholar 1 day ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 16 days ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Scholar 5 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Scholar 7 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 7 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 10 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 3 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For C: what does a log 2-fold change values of mean ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 6 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 7 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 7 months ago, created an answer that has been accepted. For A: List of all GO terms
Popular Question 7 months ago, created a question with more than 1,000 views. For ABySS fails to write out coverage.hist file and stops
Teacher 8 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
Scholar 8 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 8 months ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares

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