User: Buffo
Buffo • 1.6k
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Posts by Buffo
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Answer:
A: sam flag count
... [Decoding sam flags][1]
[ Edited link (https://www.biostars.org/u/25721/) ]
[1]: http://broadinstitute.github.io/picard/explain-flags.html ...
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... No, TMM values are the read-count normalized. With RNAseq data, you can calculate the relative abundance levels of the whole transcriptome by calculating the FPKM, RPKM or TPM, or if you have control samples you can also determine the fold of change of each transcript/gene against the control. I rec ...
written 18 days ago by
Buffo • 1.6k
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... It looks like [complexHeatmap][1]
[1]: https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/ComplexHeatmap/inst/doc/ComplexHeatmap.html ...
written 22 days ago by
Buffo • 1.6k
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... Why choose mirwalk? I recommend you to read this article: [Tools for Sequence-Based miRNA Target Prediction: What to Choose?][1] before to perform any unjustified pipeline. It summarizes the most popular and available algorithms for target prediction.
[1]: https://www.ncbi.nlm.nih.gov/pmc/articl ...
written 29 days ago by
Buffo • 1.6k
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... It looks like you do not have sequenced the entire sequence, so you can't get it. ...
written 4 weeks ago by
Buffo • 1.6k
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Comment:
C: miRna-Seq, featureCounts problem
... The mature product from these two hairpins is identical (UAGCACCAUUUGAAAUCAGUGUU) and thus indistinguishable from sequence
That is not a new debate, it is an old question about isomirs, and again, if you map your reads against mirbase files you will count multi-hit reads as single. If you consi ...
written 5 weeks ago by
Buffo • 1.6k
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Comment:
C: miRna-Seq, featureCounts problem
... So given a miRNA with two identical copies in the genome
No sense! it does not exist. You don't understand what redundant sequence is.
but we have no way of knowing which copy it came from?
Yes, we can, mapping to the genome.
Fair enough, we have been mapping to Rfam rather than mirb ...
written 5 weeks ago by
Buffo • 1.6k
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Comment:
C: miRna-Seq, featureCounts problem
... If miR-X is encoded in two places in the genome, then a read from miR-X will always be multi-mapped.
That is exactly why you should use bowtie instead of bowtie2 and sequences of high quality.
Pipelines will then either ignore this read, or count it twice (once for miR-Xa and miR-Xb)
I p ...
written 5 weeks ago by
Buffo • 1.6k
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... In addition to i.sudbery answer, I recommend you to map the reads against the genome, not against the mature/hairpin sequences. This second pipeline cause biased analysis since some of the actually known miRNAs are redundant in sequence (especially in mouse). ...
written 5 weeks ago by
Buffo • 1.6k
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... Having an internet connection is a very different thing of having a connection to a private server. But additionally, if you spend money in an NGS experiment why not spend a bit more contacting a professional bioinformatics analyst? NGS projects may be translated into large and interesting results i ...
written 7 weeks ago by
Buffo • 1.6k
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For piRNA target-interaction database?
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