User: Fabio Marroni
Fabio Marroni • 2.1k
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Posts by Fabio Marroni
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... 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 Marroni • 2.1k
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... 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 Marroni • 2.1k
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... 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 Marroni • 2.1k
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... 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 Marroni • 2.1k
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... 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 Marroni • 2.1k
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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 Marroni • 2.1k
1
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245
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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 Marroni • 2.1k
1
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... 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 Marroni • 2.1k
0
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150
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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 Marroni • 2.1k
0
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1.1k
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2
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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 Marroni • 2.1k
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