User: Buffo
Buffo • 1.2k
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Posts by Buffo
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... Keeping in mind that there is no method to sequence just miRNAs and exclude other kind of short RNAs, if you consider 20M too high for human... go ahead, personally I do not think so. ...
written 9 weeks ago by
Buffo • 1.2k
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... It depends of your specie of interest and expected miRNAs to calculate the coverage needed. And also of what you want to analyze, , for example, to analyze expression (in mouse) 20M would be enough, However, to distinguish between isomirs and/or look for new probable miRNAs you will need more cover ...
written 9 weeks ago by
Buffo • 1.2k
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Comment:
C: miRNA alignment using bowtie 2
... Since your high alignment rate may be no surprinsing, you would check if your reads really correspond to miRNAs, short RNA is not a miRNA by default, but also I recommend you to perform ungapped alingnments with bowtie2 or use Bowtie(1) to avoid isomirs. ...
written 10 weeks ago by
Buffo • 1.2k
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Comment:
C: Circular Genome Alignment
... bwa has the option to apply soft and hard clipping, it may be usefull, or hisat2 by default performs spliced alignments. ...
written 10 weeks ago by
Buffo • 1.2k
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... [mirDeep][1] works fine, but do not use it until you have read and understand the manual and protocol to predict new miRNAs. Small RNAs are not miRNAs by default.
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553977/ ...
written 12 weeks ago by
Buffo • 1.2k
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... [prinseq][1] can remove duplicated sequences. If you have a high levels of read-duplication you may consider to remove them, if not, I think that use arbitrary filters may cause absolutely biased analysis.
[1]: http://prinseq.sourceforge.net/manual.html ...
written 12 weeks ago by
Buffo • 1.2k
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374
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Comment:
C: Aligning miRNA reads to miRbase
... $cat hairpin.fa mature.fa > both.fa ...
written 3 months ago by
Buffo • 1.2k
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374
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Comment:
C: Aligning miRNA reads to miRbase
... I recommend you to use both, mature and hairpin because you may found new miRNA variants or "isoforms". And also, recommend you to use bowtie (no bowtie2 or blast) to align them, it is easy to handle and filter multihits. ...
written 4 months ago by
Buffo • 1.2k
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... Thanks Pierre :D, exactly what I cant see in front my eyes. ...
written 4 months ago by
Buffo • 1.2k
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... Hi,
By default IGV indicates insertions with respect to the reference with a purple I, and I would like to hide it or change the color, I have read the manual and it is making me crazy, I can´t find the way to do it, somebody knows if it is possible? ...
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