User: Fabio Marroni
Fabio Marroni • 1.8k
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Posts by Fabio Marroni
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... How many replicates do you have per condition?
Do you see very high variation between replicates?
Did you try doing the analysis with a toy data set (probably provided by the package developer) to see if using that you got significant results?
Are there additional software packages you may try t ...
written 14 days ago by
Fabio Marroni • 1.8k
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Comment:
C: error assembly megahit
... I am sorry... I don't know what to do. For me it works :-(
However, try to change the way you feed the read name to megahit. Maybe, if you have a few files, you can start by feeding the names by hand and then when you will have figured out the correct way to feed the names you can use automated scr ...
written 17 days ago by
Fabio Marroni • 1.8k
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Comment:
C: error assembly megahit
... Sorry... I don't understand what you mean by "it seems that you do not recognize the key and change it by parentheses, but I have a error"
Let's debug step by step:
try this and let me know if this gives an error.
mkdir test_dir
cd test_dir
touch sample1_1.fq sample1_2.fq sample2_1. ...
written 17 days ago by
Fabio Marroni • 1.8k
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C: Indel calling from sanger reads
... When I worked on Sanger sequencing I used [phred/phrap/consed][1] and that was great for finding indels. You might give that a try.
[1]: http://www.phrap.org/phredphrapconsed.html ...
written 17 days ago by
Fabio Marroni • 1.8k
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... I am not very expert of this, but maybe you can try with the so-called zero-inflated approaches?
Like something discussed in this paper: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000400008
...
written 17 days ago by
Fabio Marroni • 1.8k
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Answer:
A: error assembly megahit
... You are sending the wrong file names.
From the error message I understand that megahit is looking for the file "assembly_sample1_1.fq_1.fq", which doesn't exist
Try this:
for i in *_1.fq
do
read1=${i/.fq/}
read2=${read1/_1/_2}
/home/fernado/megahit/megahit -1 $read1 -2 $read2 ...
written 17 days ago by
Fabio Marroni • 1.8k
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... Thank you for posting! However, since this is a course/training announcement, I think it should be under News rather than under Jobs. ...
written 27 days ago by
Fabio Marroni • 1.8k
0
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... As a course organizer, I usually post the courses I organize here on Biostars, under the "News" category. Sadly enough, looks like there is no way to only view results belonging to the "News" category as is possible, e.g. for "Jobs" or "Tools". Thus I have no better suggestion than to perform a clas ...
written 6 weeks ago by
Fabio Marroni • 1.8k
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119
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... ![enter image description here][1]
We are happy to accept registrations for this practical course on the analysis of NGS data related to epigenetics. The main topcis that will be covered are: analysis of bisulfite sequencing (BS-seq) data, analysis of ChIP-seq data, analysis of small RNAs, analysis ...
written 6 weeks ago by
Fabio Marroni • 1.8k
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235
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... Great suggestion! I will try to make good use of it! However, I have to confess that in origin I named the three days "Welcome to the Jungle", "Patience" and "Paradise City", respectively. ...
written 3 months ago by
Fabio Marroni • 1.8k
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