User: Fabio Marroni
Fabio Marroni • 2.6k
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- http://www.fabiomarron...
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- Joined:
- 9 years, 6 months ago
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Posts by Fabio Marroni
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... It is indeed strange that your reference contains the letter M. As a first step I would double check that the reference contains nucleotides and not amino acids. Once you are sure that this is the case you can use pyfasta of some other tool depending in which programming language you are proficient. ...
written 6 days ago by
Fabio Marroni • 2.6k
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... You can give a look at this post in which I encountered a similar issue: https://www.biostars.org/p/293353/
However, the short answer is: yes, it can be right.
topGO can add terms due to hierarchical structure. I think it is mostly ok, but maybe is not ideal, and that's why I sometimes use a fishe ...
written 16 days ago by
Fabio Marroni • 2.6k
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... You could just perform correlation of log2FC in the two analysis, preferably using Spearman's correlation, instead of Pearson's. Also, if you perform a Wilcoxon test between the 2 log2FC distributions you can test if they look the same. You can also do the same with the padj distributions. ...
written 16 days ago by
Fabio Marroni • 2.6k
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... Your guess is correct. You can give a look at [this paper][1], in which some information about the nature of the environmental sample category is given. Baiscally the author states that *environmental samples* "are sequences that have been recovered directly from the environment, with no direct know ...
written 19 days ago by
Fabio Marroni • 2.6k
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2.3k
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Comment:
C: how to caculate enrichment score
... It's just flipped: 1/(0.92)=1.0869 which is basically what is reported in the paper ...
written 27 days ago by
Fabio Marroni • 2.6k
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... In addition to [genomax][1]'s suggestion: what is the output of the command: `echo $db` ? Is the variable defined and pointing to an existing file? However, my suspect number 1 is the one pointed out by [genomax][2], i.e. the fact that the file `orf_trans.fasta` is not in the current directory. You ...
written 5 weeks ago by
Fabio Marroni • 2.6k
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102
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Comment:
C: Error in Trinity Process
... You can't ask 800G of RAM if you have 500G. This is probably why it gets killed. Try asking for 480G. ...
written 5 weeks ago by
Fabio Marroni • 2.6k
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116
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... I saw a couple of posts suggesting to restart your R session and try again; it may be worth a try!
https://community.rstudio.com/t/error-message-lazy-load-database-keras-rdb-is-corrupt/24381
https://github.com/thomasp85/patchwork/issues/36 ...
written 5 weeks ago by
Fabio Marroni • 2.6k
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... Try `samtools faidx ./file_1.fasta -i MHLFILTNLILPAFEDLAQG` or `samtools faidx -i ./file_1.fasta MHLFILTNLILPAFEDLAQG` ...
written 3 months ago by
Fabio Marroni • 2.6k
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235
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Comment:
C: samtools subsampling reads
... The pattern is perfectly fine, and statistically expected. Highly covered regions in the original genome, are also more likely to be sampled by random sampling, so you will always (more or less) keep the same pattern of coverage, but at lower levels. ...
written 3 months ago by
Fabio Marroni • 2.6k
Latest awards to Fabio Marroni
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5 weeks ago,
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For Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Heritability of pigmentation traits
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8 months ago,
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For topGO is performing enrichment test on GO terms that are not present in my dataset
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17 months ago,
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For A: what does Num_Probes in a segmentation file refer to?
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18 months ago,
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For Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions
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19 months ago,
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For A: what does Num_Probes in a segmentation file refer to?
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19 months ago,
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For A: What Is Ivsi Number Of A Mutation?
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For Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions
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22 months ago,
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For A: what does Num_Probes in a segmentation file refer to?
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For Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions
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For A: What Is Ivsi Number Of A Mutation?
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For A: what does Num_Probes in a segmentation file refer to?
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For Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions
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2.5 years ago,
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For A: What Is Ivsi Number Of A Mutation?
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For A: What Is Ivsi Number Of A Mutation?
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For A: What Is Ivsi Number Of A Mutation?
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For A: what does Num_Probes in a segmentation file refer to?
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For A: What Is Ivsi Number Of A Mutation?
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For A: what does Num_Probes in a segmentation file refer to?
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3.2 years ago,
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For A: what does Num_Probes in a segmentation file refer to?
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3.2 years ago,
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For A: What Is Ivsi Number Of A Mutation?
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For A: what does Num_Probes in a segmentation file refer to?
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3.3 years ago,
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For A: What Is Ivsi Number Of A Mutation?
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