User: Fabio Marroni
Fabio Marroni • 2.7k
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Posts by Fabio Marroni
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... 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 Marroni • 2.7k
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... 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 Marroni • 2.7k
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... 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 Marroni • 2.7k
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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 Marroni • 2.7k
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... 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 Marroni • 2.7k
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... 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 Marroni • 2.7k
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... 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 Marroni • 2.7k
0
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201
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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 Marroni • 2.7k
0
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460
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... 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 Marroni • 2.7k
0
votes
1
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116
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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 Marroni • 2.7k
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