User: Antonio R. Franco
Antonio R. Franco • 3.6k
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- Spain. Universidad de Córdoba
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Posts by Antonio R. Franco
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... I run Clustal Omega to get a cladogram
Clustal Omega uses a HMM algorithm to cluster sequences together
By the other hand, there are many programs to run bootstrapping with the alignments. One os such is IQ-Tree, which is fast, sensitive, and available locally or through a WEB server
However, I d ...
written 9 days ago by
Antonio R. Franco • 3.6k
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Answer:
A: short RNA reads alignment
... The database you align with depends on your interest. Choose the best suitable for your purpose since you can map virtually with any sequences you want
In relation to size, [take a look to this thread][1]. You can do it and even change some settings for your interest
[1]: https://www.biostars.or ...
written 13 days ago by
Antonio R. Franco • 3.6k
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Comment:
C: Remove singletons from bam
... If you have this error when running the samtools command is that the original file is corrupted. If dealing with the final filtered file, give it a little time to finish the command. I have just tested the command and is working nicely
...
written 16 days ago by
Antonio R. Franco • 3.6k
1
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Answer:
A: Remove singletons from bam
... Take a look to this page
[https://broadinstitute.github.io/picard/explain-flags.html][1]
Then try to use samtools view with the -f and the -F options to select those mapped reads that are of your interest.
If you have mapped paired reads, all your BAM flags will be an odd number, meaning that they ...
written 16 days ago by
Antonio R. Franco • 3.6k
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... The first one is the fasta file corresponding to the genome
The second one is the annotation of the first file
I don't understand your third question. Significance of preparing for primary assembly in RNASequencing?
These files are already assembled..
If you want to assemble again, you need to use ...
written 16 days ago by
Antonio R. Franco • 3.6k
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... Can you actually get this kind of information from a MA plot ?
> The plot suggests that the variance of the individual transcriptomic
> experiments is high and that a high number of genes in the plot
> biological replicates show high standard deviations and are out of the
> range for re ...
written 20 days ago by
Antonio R. Franco • 3.6k
• updated
20 days ago by
Devon Ryan ♦ 78k
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... To date (March 2018) you can install a GUI into your WSL (WSL is the Windows Linux System without problems. Several links [like this one][1] can be followed
[1]: https://github.com/Microsoft/WSL/issues/637 ...
written 5 weeks ago by
Antonio R. Franco • 3.6k
0
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129
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... I mentioned that. I am mapping BS-Seq sequences with Bismark
...
written 7 weeks ago by
Antonio R. Franco • 3.6k
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129
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... You are right. They have the same number of reads
...
written 7 weeks ago by
Antonio R. Franco • 3.6k
3
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2
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129
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2
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... I am getting BAM files with Bismark mapping with bowtie2. This gives you an unordered BAM file
Thus, I am sorting the BAM file with the command
> samtools sort -O bam -T tmp_ -o Name_sorted.bam Unordered.bam
The unordered bam file can have a 2,6Gb size, but the ordered one drops down to 1,2Gb. ...
written 7 weeks ago by
Antonio R. Franco • 3.6k
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13 days ago,
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For A: Must know algorithms before attending a bioinformatics interview
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29 days ago,
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For A: is there any databse that provides the promoter of a specific gene?
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For C: Why mate-Paired end, Paired-end and Single End reads library to be combined for
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For A: is there any databse that provides the promoter of a specific gene?
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For A: is there any databse that provides the promoter of a specific gene?
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For A: is there any databse that provides the promoter of a specific gene?
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