User: Fabio Marroni

gravatar for Fabio Marroni
Fabio Marroni2.6k
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Italy
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http://www.fabiomarron...
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Last seen:
17 hours ago
Joined:
9 years, 6 months ago
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Posts by Fabio Marroni

<prev • 423 results • page 1 of 43 • next >
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Comment: C: Can't load reference sequence from file 'GRCh37.fa': Unexpected character 'M' fo
... 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 Marroni2.6k
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Comment: C: GO enrichment: enriched term was not assigned to all genes in functional annotat
... 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 Marroni2.6k
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Comment: C: Correlation between 2 deseq2 outputs? how to best do it?
... 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 Marroni2.6k
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Answer: A: what is environmental sample (Taxonomy ID: 61964) in NCBI?
... 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 Marroni2.6k
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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 Marroni2.6k
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Answer: C: Blastdbcmd (Windows) - Too Many Positional Arguments
... 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 Marroni2.6k
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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 Marroni2.6k
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Answer: A: Can't find fstat() and pairwise.fstat()
... 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 Marroni2.6k
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Comment: C: Samtools faidx not printing reverse complement
... Try `samtools faidx ./file_1.fasta -i MHLFILTNLILPAFEDLAQG` or `samtools faidx -i ./file_1.fasta MHLFILTNLILPAFEDLAQG` ...
written 3 months ago by Fabio Marroni2.6k
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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 Marroni2.6k

Latest awards to Fabio Marroni

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Heritability of pigmentation traits
Popular Question 8 months ago, created a question with more than 1,000 views. For topGO is performing enrichment test on GO terms that are not present in my dataset
Scholar 17 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 19 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 22 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.0 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 3.1 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 3.2 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 3.2 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 3.3 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?

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