User: lieven.sterck

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lieven.sterck1.9k
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Posts by lieven.sterck

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Comment: C: Replacement for Tribe-MCL?
... You could have a look into for instance [orthomcl][1] or orthoFinder (newer) . They should do a fairly similar thing as Tribe-MCL, though not exactly the same as they are more focused on finding "orthologs" (in laymen terms: they tend to cluster more tightly giving smaller/stricter cluster/gene-fams ...
written 1 day ago by lieven.sterck1.9k
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Comment: C: Replacement for Tribe-MCL?
... Are you specifically looking for an (exact) replacement of tribe-mcl or would any other protein clustering do as well? ...
written 3 days ago by lieven.sterck1.9k
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Comment: C: GREP: out of memory
... Where did you get your files from, which operating system? Did you open them in windows or so? I had to look myself but apparently this 'error' is related to the encoding of your file. If you have dos2unix (or mac2unix) installed, you might run that first on your files to convert them to proper un ...
written 7 days ago by lieven.sterck1.9k
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Comment: C: GREP: out of memory
... before the `-wF` part. I must add that I mentioned this in thinking you only needed one line per grep but that's likely not the case. So it might be a bit tricky to use the `-m` option ...
written 7 days ago by lieven.sterck1.9k
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Comment: C: CDS sequence from mRNA and protein sequence
... OK, I'll add some to my 'answer' My general advise would be to go for one that does nothing more than to look for the longest orf, so preferentially none that use coding potential or such but simply (and bluntly) gets the longest one from a potential start to a stop (by limiting to the forward stra ...
written 9 days ago by lieven.sterck1.9k
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Answer: A: CDS sequence from mRNA and protein sequence
... Simply run some software on it get the longest ORF (plenty of tools around for that) from the mRNA, should (in theory) end up to the proteins. Additionally just double-check them against your protein set (eg calculate MD5 key and compare both). potential software to use: - some custom python scri ...
written 9 days ago by lieven.sterck1.9k
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Comment: C: Software for Genome Annotation
... or this review: [Ten steps to get started in Genome Assembly and Annotation][1] [1]: https://f1000research.com/articles/7-148/v1 ...
written 10 days ago by lieven.sterck1.9k
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Answer: A: Software for Genome Annotation
... it all depends a little on your expertise and/or your ultimate goal. if you want to have a quick look at the gene content, then tools like Maker, Maker-P etc will do. They are more of less "plug-and-play" kinda solutions without much expertise required if on the other hand you're looking for a hig ...
written 10 days ago by lieven.sterck1.9k
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Comment: C: What is the prefered script for HISAT2 genome-guided approach? --dta, --ss , --e
... I don't think I differ a lot from what https://www.biostars.org/u/18713/ is telling you. If it is in the manual I might as well consider to (re-)run it the --ss and --exon activated (for the genome index building). I merely wanted to point out that if, for some reason, you don't have the required i ...
written 10 days ago by lieven.sterck1.9k
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Comment: C: GREP: out of memory
... Can you give us an idea of the numbers we're talking about here? file sizes? list length ? For most cases a solution like offered by https://www.biostars.org/u/22075/ (== loop through your list and grep each of them) will solve your issue ...
written 10 days ago by lieven.sterck1.9k

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Scholar 12 days ago, created an answer that has been accepted. For A: List of all GO terms
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Teacher 4 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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