User: Fabio Marroni

gravatar for Fabio Marroni
Fabio Marroni2.2k
Reputation:
2,190
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Location:
Italy
Website:
http://www.fabiomarron...
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Last seen:
11 hours ago
Joined:
7 years, 11 months ago
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Posts by Fabio Marroni

<prev • 350 results • page 2 of 35 • next >
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Comment: C: How do I know if I have DNA contamination in RNA-seq data?
... Basically, you have tried almost everything. I would suggest a massive effort on step 3. For example you might count the number of reads that align over introns in all your samples. The higher the number of such reads the higher the DNA contamination (assuming that the proportion of pre-mRNA in you ...
written 12 weeks ago by Fabio Marroni2.2k
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Comment: C: Bash: For loop with two statements, first statements as input to second with .fa
... It looks fine. What is the error you get? Also, the line starting with "canu" should be on a new line. ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: R packages error.
... Ok, [Devon][1] already solved the problem... Thanks Devon, I might need this trick!!! [1]: https://www.biostars.org/u/7403/ ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: R packages error.
... HI Francis, I think that the category tool is for announcing tools that you are making available, not for asking questions regarding tools (everybody is asking questions regarding a bioinformatics tool, more or less!) Not having root permission complicates things. Looks like you have some problems ...
written 3 months ago by Fabio Marroni2.2k
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Answer: A: Is there any way to merge intervals based on a minimum overlap?
... I think you can use bedtools [intersect][1], with the -f (minimum fraction of overlap) or -r (reciprocal overlap) option. In the worse case you just can use bedtools intersect, ask to print the length of overlap and then remove all the instances in which the overlap is shorter than your threshold. M ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: How to use qqman using own data?
... It is written in the first page of the manual: they are "Simulated GWAS results as obtained from plink --assoc." You can find the manual [here][1] [1]: https://cran.r-project.org/web/packages/qqman/qqman.pdf ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: refseq NC id list download
... Works pretty well, although with >10,000 entries you might be obliged to split queries (you might get a "bad gateway" error). My longest download consisted of slightly more than 5000 entries. ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: Many 0 in ped file converted from vcf genomic data
... The reason is that you have too many missing genotypes (presumably all the zeros). How many missing data are there in the vcf? How much missing data is tolerated with your plink command? It can be a problem in conversion, or maybe the vcf had a lot of missing data. ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: Many 0 in ped file converted from vcf genomic data
... I agree with [ATpoint][1]: this would make your example more readable. Also, it would be helpful if you posted the corresponding line of the vcf so that we can see if there was a problem in the converison. [1]: https://www.biostars.org/u/25721/ ...
written 3 months ago by Fabio Marroni2.2k
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Comment: C: How to merge read count of multiple sample in one fiel to be used for DESeq2 fol
... DESeq2 has several features for importing data: did you give a look to them? You can find them [here][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#input-data ...
written 3 months ago by Fabio Marroni2.2k

Latest awards to Fabio Marroni

Scholar 19 days ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 4 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 6 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 13 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 18 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 19 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 20 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 20 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 21 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
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Scholar 22 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Scholar 2.6 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?

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