User: Iñigo Prada

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Posts by Iñigo Prada

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How does CIRCexplorer2 work with paired-end data?
... Yeah, I know (I have use it and I got very interesting results). My question is how does it work theoretically with paired-end data. Does it aim to identify only backspliced junction reads? Or does it take another kind of information into account? like in this case: """" The right part of the read ...
written 2 days ago by Iñigo Prada0
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Comment: C: converting Indel Realigned Bam to fastq
... I will check that! Thanks! ...
written 7 days ago by Iñigo Prada0
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Comment: C: converting Indel Realigned Bam to fastq
... Hi Pierre! thank you! Yeah, I guess that they must have remove duplicates, I will write to the company that did the first analysis and see what is going on. Thanks! ...
written 7 days ago by Iñigo Prada0
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converting Indel Realigned Bam to fastq
... Hi everyone! My lab is working on an exome-seq pipeline and I have been given the bam files after performing Indel realignment. I want to perform again all the pipeline as sanity check. I have converted the bam files to fastq using Picard SamtoFastq and when performing the quality control of the ...
next-gen exome-seq written 9 days ago by Iñigo Prada0 • updated 9 days ago by igor3.1k
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Detecting non-exonic conserved regions
... Hi! I am trying to detect conservation in non exonic regions of the human genome. What I have is is a bed file obtained from the UCSC genome browser Cons Indels MmCf Track. This track shows conserved regions in the genome. When I displayed the file in the genome browser, I can see that there are re ...
bed signal detection written 6 weeks ago by Iñigo Prada0 • updated 6 weeks ago by Chirag Nepal1.7k
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Comment: C: Run transmembrane prediction with one multifasta file and multiple MSA sequences
... Do you have any knowledge using a programming language (python for example)? ...
written 6 weeks ago by Iñigo Prada0
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Answer: A: Tophat vs Tophat-fusion concordant alignment rate
... Tophat fusion removes reads that map to more than two places in the genome, thus, the tophat mapping percentage can be higher because it won't remove multimappers by default ...
written 6 weeks ago by Iñigo Prada0
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How does CIRCexplorer2 work with paired-end data?
... Hi everyone! I have been using CIRCexplorer2 in single-end RNA sequencing datasets for a while, however, I have never use it for paired end data. In the papers and suplementary methods of circexplorer and circexplorer2 it is clearly explained how does the program identify circRNA in single-end data ...
tophat circrna rna-seq written 6 weeks ago by Iñigo Prada0 • updated 3 days ago by kepbod70
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Comment: C: fastqc overrepresented sequences
... yeah, my question is why fastqc misses that sequence when I run my fastq file without removing the first 30 nucleotides. My guess is that it should appear in as an overrepensented sequence before removing the first 30 nucleotides ...
written 12 weeks ago by Iñigo Prada0
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Comment: C: fastqc overrepresented sequences
... The data comes from 4C-seq. Basically, for a known chromosomic position, we crosslink the region that its interacting with the this known region. Then, this is digested with two restriction enzymes and it is sequenced. In this case, it was sequenced in an Ion Torrent machine ...
written 12 weeks ago by Iñigo Prada0

Latest awards to Iñigo Prada

Scholar 6 weeks ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 6 weeks ago, has more than 80 characters in the information field of the user's profile.

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