User: Lorena Pantano

gravatar for Lorena Pantano
Reputation:
360
Status:
Trusted
Location:
Barcelona
Website:
http://www.vpantano.name/
Scholar ID:
Google Scholar Page
Last seen:
4 years, 10 months ago
Joined:
7 years, 11 months ago
Email:
l*************@gmail.com

I got my Biochemestry degree in 2005, and moved to Bioinformatics after that. I have a Msc in Bioinformatics for Health Sciene and PhD in Biomedicine (2008 and 2011, Pompeu Fabra University). I am very interesting in small RNAs, and epigenetics. My tools to analyze HTD is python, R, and linux commands. Although I learnt Java, perl and C as well. My little hobbies are robotics, web applications and smartphone applications. And of course, Udacity and Coursera.

Posts by Lorena Pantano

<prev • 53 results • page 1 of 6 • next >
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Answer: A: Problem with Fastqc quality control for miRNAseq data
... Hi! Well, don't know if it is really a problem. normally in miRNA data, there are a bunch super highly expressed, and then the rest. That means that the time each miRNA is represented is a lot. I guess you see something weird with duplication figure as well? Fastqc was designed for DNAseq, which y ...
written 4.9 years ago by Lorena Pantano360
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Comment: C: miRdeep2 mapper error
... HI, I think is like the alignment is empty, there is any temporary file directly from bowtie, any map or sam file? That part of the code is counting how many hits you have, but since it never enter the loop. btw: answer should be only answer to the question, anything like comments, should be added ...
written 5.0 years ago by Lorena Pantano360 • updated 7 months ago by RamRS27k
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Comment: C: mRNAs targeted by list of miRNAs
... Hi, this is quite challenging due to the large false positive you get when getting targets without having more information. If you do only this, probably your 'top genes' will be biased to long 3UTR genes and most study miRNAs.  I will try to get all targets for each miRNA, count how many miRNAs t ...
written 5.0 years ago by Lorena Pantano360
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Comment: C: miRNA mapping rate is very low.. (less than 0.03%)
... Hi, glad the analysis starts working. You can filter the one mapping to mmu* miRNAs and quantify how many you have just to make you an idea if seems are good now. It is normal to get hits to other miRNAs, more in conserved miRNAs, so you should be an enriched of reads with hits at mmu* if you count ...
written 5.0 years ago by Lorena Pantano360
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Comment: C: miRNA mapping rate is very low.. (less than 0.03%)
... Did you do the index for hairpin.fa? I use to change U by T, but not sure if it does automatically. If you only want to map to mirbase you can use miraligner:. You can download from here: https://github.com/lpantano/seqbuster/raw/master/modules/miraligner/miraligner.jar and the usage is:  java -j ...
written 5.0 years ago by Lorena Pantano360
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Answer: A: miRNA sequencing question
... Hi Alan, I think they used miRDeep2 and I think it just counts all reads in all places.  About assuming that the proportion of precursors it should be similar to the proportion of the mature ... well, it is difficult to say. It could be one mature/precursor is more stable than other, so it risky t ...
written 5.2 years ago by Lorena Pantano360
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Answer: A: Analyze miRNA microarrays
... Hi, I am not an expert but starting with this package may help: http://master.bioconductor.org/packages/release/bioc/vignettes/AgiMicroRna/inst/doc/AgiMicroRna.pdf A good normalization will show similar intensity distribution and clustering the samples by replicates for instance. In arrays in gen ...
written 5.2 years ago by Lorena Pantano360 • updated 5.2 years ago by Neilfws48k
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Comment: C: Transform smallRNA SRA (Illumina) sequences to FASTA
... there are some adapter removal that are specific for mRNA and not small RNA. I would use cutadapt. The adapter in smallRNA is always the same, and it is enough to detect 8 nucleotides. The adapter should be something like AGATCGGAAGAGCAC, or without the first A if it is standard protocol. Fastqc was ...
written 5.4 years ago by Lorena Pantano360
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Comment: C: BLAT does appear anything in the results but blat worked.
... I think this is only if you don't change tilesize, stepsize, and the rest of parameters. I am getting 13 nt match changing those to very low values. Make sure the database is DNA (not Us). ...
written 5.5 years ago by Lorena Pantano360
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Answer: A: BLAT does appear anything in the results but blat worked.
... Hi, you can try to add -minMatches=1 -minScore=10 -minIdentity=50 Al well, you can generate a test data with some mature miRNA in mirbase.fa, to check is giving you some hits, and as well, modifying this example with some mis-matches or doing only that half of the sequence is identical to the miRN ...
written 5.5 years ago by Lorena Pantano360

Latest awards to Lorena Pantano

Scholar 5.2 years ago, created an answer that has been accepted. For A: How do you classify the miRNAs? What is the best way to classify miRNAs hypothet
Scholar 5.5 years ago, created an answer that has been accepted. For A: How do you classify the miRNAs? What is the best way to classify miRNAs hypothet
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: identifying miRNA in RNAseq
Scholar 5.5 years ago, created an answer that has been accepted. For A: How do you classify the miRNAs? What is the best way to classify miRNAs hypothet
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: identifying miRNA in RNAseq
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: identifying miRNA in RNAseq
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: identifying miRNA in RNAseq
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: identifying miRNA in RNAseq
Autobiographer 6.3 years ago, has more than 80 characters in the information field of the user's profile.

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