User: Lídia

gravatar for Lídia
Lídia80
Reputation:
80
Status:
New User
Location:
Spain
Last seen:
3 years, 12 months ago
Joined:
6 years, 11 months ago
Email:
l************@estudiant.upf.edu

Posts by Lídia

<prev • 10 results • page 1 of 1 • next >
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Answer: A: How To Convert Vcf File To Plink Ped Format?
... I have read that GATK has also a tool to do this conversion. It is called VariantsToBinaryPed. I have not used it yet but it looks useful and I will give it a try!  (https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_VariantsToBinaryPed.html)     ...
written 4.0 years ago by Lídia80
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Comment: C: samtools view region vs. bamtools filter region
... The addition of both terms + the interaction... ;-)  ...
written 4.1 years ago by Lídia80
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Comment: C: samtools view region vs. bamtools filter region
... Sorry for such a silly mistake... You were completely right!  filter -region 3R:15000000..15100000 -in IV75_realigned_reads.bam -out test.bam bamtools count -in test.bam  #28034   Thank you very much for your answer  ...
written 4.1 years ago by Lídia80
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samtools view region vs. bamtools filter region
... When extracting reads aligned to a certain region, what is the difference between using samtools view and bamtools filter region? Here is the code and the counts of the number of reads recovered. I don't understand why the number of reads recovered are so different between the two approaches. Any h ...
ngs bam samtools bamtools written 4.1 years ago by Lídia80 • updated 4.1 years ago by Pierre Lindenbaum111k
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Comment: C: R/Bioconductor And .Chp Files
... Thank you very much! It was very easy to import the data from ArrayExpress and I could do some basic manipulations following the vignette and the reference manual instructions so at the end I could extract the information I needed. ...
written 5.3 years ago by Lídia80
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Comment: C: R/Bioconductor And .Chp Files
... Thank you! These links were very helpful. Specially the second and third one. At the end I started from the raw files and I could check what I was looking for :D ...
written 5.3 years ago by Lídia80
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R/Bioconductor And .Chp Files
... Hi all I want to extract the level of expression of two genes from the microarray data deposited here. The available files are the following: Investigation description E-MEXP-1594.idf.txt Sample and data relationship E-MEXP-1594.sdrf.txt Raw data (2) E-MEXP-1594.raw.1.zip, E-MEXP-1594.ra ...
microarray written 5.3 years ago by Lídia80 • updated 5.3 years ago by Martin Morgan1.6k
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Comment: C: Poly(A) Signal Prediction And Forward/Reverse Strand Conventions
... Thank you, thank you, thank you!! :D I am a Biology student and, despite being very interested in bioinformatics, I don't know much about it! I'm very eager to learn more! ...
written 7.0 years ago by Lídia80
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Comment: C: Poly(A) Signal Prediction And Forward/Reverse Strand Conventions
... Thanks for your answer! I wasn't talking about de poly-A or poly-T but the consensus signal that is located 10-30 nucleotides upstream from it. When pre-mRNA is processed an enzyme cleaves the mRNA 10-30nt downstream from the poly(A) signal which usually is 5'-AAUAAA-3'. The sequence itself isn't re ...
written 7.0 years ago by Lídia80
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Poly(A) Signal Prediction And Forward/Reverse Strand Conventions
... Hi! It's my first time here and I really thank you all for the usefull content you submit. I read a couple of questions about forward and reverse convention and it really came as a grate relief to see that I wasn't the only person who was wondering about such a basic but sometimes confusing thing. ...
written 7.0 years ago by Lídia80 • updated 7.0 years ago by Steve Lianoglou4.9k

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Popular Question 7.0 years ago, created a question with more than 1,000 views. For Poly(A) Signal Prediction And Forward/Reverse Strand Conventions

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