User: Fabio Marroni

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Fabio Marroni2.7k
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9 years, 9 months ago
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Posts by Fabio Marroni

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Comment: C: differential expression- coding genes
... So Rob... Now that you know that it is hard to define TUNAR as coding or not you have to tell us why it is so important for you to know!!! ...
written 23 days ago by Fabio Marroni2.7k
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Comment: C: differential expression- coding genes
... It is true!!! It is simply that [genecards][1] and [ENTREZ][2] list the gene as non-coding, probably as a consequence of the first papers listing it as a non-coding. [1]: https://www.genecards.org/cgi-bin/carddisp.pl?gene=TUNAR [2]: https://www.ncbi.nlm.nih.gov/gene/100507043 ...
written 23 days ago by Fabio Marroni2.7k
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Comment: C: differential expression- coding genes
... I assume you are working on human. TUNAR is a long non-coding RNA which means that the gene is transcribed as RNA, but not translated to protein, so it is perfectly normal that you identify it. **EDIT:** I just read that you stated that your data are protein coding genes. So, you should double che ...
written 23 days ago by Fabio Marroni2.7k
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Comment: C: gffcompare input file
... If I well understand the help line, you should provide a text file in which you write the **names** of the gtf files you want to compare. You don't need to convert the gtf files to text (BTW: gtf **are** indeed text files, that follow some format rules). ...
written 27 days ago by Fabio Marroni2.7k
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Comment: C: normalization RNASeq Data for QTL analysis
... I found some advice on matrixeQTL [faq][1]: If you go to the "Outliers in expression. Quantile normalization and Kruskal-Wallis test." paragraph, they also suggest some R code for the normalization. [1]: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/faq.html ...
written 27 days ago by Fabio Marroni2.7k
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Comment: C: Gene Enrichment (GO) and KEGG analysis problems
... Which organism? > some sets of genes that was given in a form .txt without their gene IDs I hope they gave you some sort of gene names. Try to search for the gene names that are in your txt file in RefSeq and ncbi and see if you are able to convert them to the convention required by clusterPro ...
written 29 days ago by Fabio Marroni2.7k
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Comment: C: EXITING: because of fatal INPUT file error: could not open read file
... I think that [GenoMax][1] got the issue. To answer your questions, the generated files are mostly log files (in which you will probably find the error messages again and the command you issued). The file `Aligned.out.sam`, which is the first result you should obtain, is indeed empty (see the 0 on th ...
written 7 weeks ago by Fabio Marroni2.7k
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Comment: C: Ploidy in R
... Hi sharihba! Your question is rather vague. A first step would be to read [instructions][1] on how asking good questions on biostars. In addition, you should provide more info, i.e. how is exactly your bedcov formatted, which organism are you talking about, what did you try, and so on... [1]: h ...
written 8 weeks ago by Fabio Marroni2.7k
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Comment: C: bedGraphToBigWig: error while loading shared libraries: libpng12.so.0: cannot op
... Do you have [conda][1] on your system? If so, you can install libpng12.so.0 via conda. [1]: https://docs.conda.io/en/latest/ ...
written 8 weeks ago by Fabio Marroni2.7k
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Answer: A: tissue specific gene list
... In the web page of GTEx there's a file described as follows: > Median gene-level TPM by tissue. Median expression was calculated from the file GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz. I guess it is good for you. You just have to select the right column. The file is [this][1] o ...
written 8 weeks ago by Fabio Marroni2.7k

Latest awards to Fabio Marroni

Appreciated 22 days ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Heritability of pigmentation traits
Popular Question 11 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 20 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 22 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.2 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 2.3 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 3.3 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?
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 3.4 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 3.5 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?

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