User: Macspider
Macspider • 2.8k
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Posts by Macspider
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... Already done, but thanks. ...
written 2 days ago by
Macspider • 2.8k
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... Might consider this. I'm working with *E. coli* so... then perhaps I can use RATT with that! ...
written 2 days ago by
Macspider • 2.8k
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... Thanks, I'll give them a try! ...
written 2 days ago by
Macspider • 2.8k
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... > I tried RATT but couldn't really use it (needs ENSEMBL IDs).
I can't use RATT sadly.
@genomax I don't necessarily trust the original annotation, I just want to give it a try if there is a simple way to transfer it, before doing my own gene prediction which is more time-consuming. ...
written 2 days ago by
Macspider • 2.8k
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... I have a FASTA genome sequence of a particular accession of a species that I'm using. It was also annotated (in terms of genes and CDS) by unknown people some unknown time ago. This genome has shown to have issues and therefore I have re-assembled it into a new genome. Of course I could run a gene p ...
written 3 days ago by
Macspider • 2.8k
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Comment:
C: RepeatModeler - FastaDB error
... Did you solve it? And how? I'm having the same issue. ...
written 6 weeks ago by
Macspider • 2.8k
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... It depends on how your library was generated, and that you should ask to who made the sequencing libraries. If they used TruSeq2 and you're using the TruSeq3 file, then you should change that. Check the files available in the `Trimmomatic` install directory. ...
written 4 months ago by
Macspider • 2.8k
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... Map your reads with your mapping software of choice (just needs to output a sam file) and then run that sam file through a feature counter, for example [HTSeq][1].
[1]: https://htseq.readthedocs.io/en/release_0.11.1/ ...
written 5 months ago by
Macspider • 2.8k
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... Is your library stranded? ...
written 5 months ago by
Macspider • 2.8k
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... I'm answering myself, for future readers:
The 4DTv ratio cannot be converted into millions of years, as it is a relative measure of time and therefore can't be converted into an absolute one.
However, one can use the *rate of substitution at neutrally evolving sites* to determine age. Basically: ...
written 5 months ago by
Macspider • 2.8k
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For Quality, MQ0F, other parameters for proper VCF filtering
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Teacher
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For A: How to convert .bed file to .juncs file using Tophat?
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For C: How to add tophat and bowtie to the path?
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For DESeq2 proper design setting
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For A: Explanation of a Perl script
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For Best way to compare two samples in a VCF file
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For C: How to add tophat and bowtie to the path?
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For Remove duplicates from reads: best practices?
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15 months ago,
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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17 months ago,
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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17 months ago,
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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18 months ago,
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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19 months ago,
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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