User: Fabio Marroni

gravatar for Fabio Marroni
Fabio Marroni2.1k
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Italy
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http://www.fabiomarron...
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19 hours ago
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7 years, 10 months ago
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Posts by Fabio Marroni

<prev • 343 results • page 1 of 35 • next >
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Answer: A: Websites for Bioinformatics openings in Germany/EU
... Some good places related to bioinformatics in Europe: - [Biostars][1] - International society for Computational Biology ([ISCB][2]) Plus some very good web-sites which are not specific for bioinformatics nor for Europe, but that may turn to be very useful if you carefully design your alerts/sea ...
written 5 weeks ago by Fabio Marroni2.1k
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Comment: C: Genotyping diploid organisms from Sanger AB1 files
... When I worked on Sanger data I used Phred/Phrap/Polyphred, and it was probably the best tool around. If you are using the results in clinical setting you might investigate the issues brought forward by genomax with your clinical colleagues. ...
written 5 weeks ago by Fabio Marroni2.1k
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Answer: A: Plant small RNA (sRNA) data analysis pipeline
... Your pipeline is reasonable. I don't know how to help regarding the indexing problem; I understand that genomes larger than the human are very hardly managed by common index building tools. You might ask to someone working on wheat, I have no experience on that. As a shortcut you might map on the tr ...
written 7 weeks ago by Fabio Marroni2.1k
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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 8 weeks ago by Fabio Marroni2.1k
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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 9 weeks ago by Fabio Marroni2.1k
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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 9 weeks ago by Fabio Marroni2.1k
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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 9 weeks ago by Fabio Marroni2.1k
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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 9 weeks ago by Fabio Marroni2.1k
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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 9 weeks ago by Fabio Marroni2.1k
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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 9 weeks ago by Fabio Marroni2.1k

Latest awards to Fabio Marroni

Scholar 3 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 5 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Sample Sam File
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Appreciated 12 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Scholar 17 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
Appreciated 18 months ago, created a post with more than 5 votes. For A: What Is Ivsi Number Of A Mutation?
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: error in R
Scholar 19 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 20 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?
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Scholar 21 months ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Scholar 2.5 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?
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Scholar 3.1 years ago, created an answer that has been accepted. For A: what does Num_Probes in a segmentation file refer to?

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