User: Geparada

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Geparada1.4k
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Cambridge
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http://bit.ly/1Mg7ioR
Last seen:
9 months, 2 weeks ago
Joined:
9 years ago
Email:
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PhD student at Welcome Trust Sanger Institute.
https://twitter.com/ge_parada

Posts by Geparada

<prev • 143 results • page 1 of 15 • next >
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Comment: C: Mapping exonic sequences across species
... Thanks a lot Eric! These articles looks very interesting, they are exactly on the spot of my question. I am happy other people is already putting efforts to implement fine-scale orthology mapping at the exon level. ...
written 11 months ago by Geparada1.4k
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Comment: C: Mapping exonic sequences across species
... any links to this "published set"? I have only seen public lists of gene homologies, but they are not at the exon level. ...
written 11 months ago by Geparada1.4k
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Comment: C: Mapping exonic sequences across species
... Hey! Thanks for your reply, however, I am looking for homologies at the exon level. But still, start cutting down the chances by the only map the exons to the homologous regions might be a good idea. ...
written 11 months ago by Geparada1.4k
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Comment: C: How do I find the same gene in two different assemblies?
... I also think generating your own chain files and use liftOver is a good shoot. Otherwise, extract the genomic sequence of each gene and then use blat or gmap to map the to the other assembly. ...
written 11 months ago by Geparada1.4k
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Comment: C: Long read alignment
... But BWA would be useful only for DNA sequencing, right? For RNA-seq I guess STAR would work nicer. ...
written 11 months ago by Geparada1.4k
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Comment: C: Seeking Freelance bioinformatician
... My bet is on `epoceire [AT] gmail [dot] com` (is this bot-proof enough). ...
written 11 months ago by Geparada1.4k
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Mapping exonic sequences across species
... Hello there, I need to find exons that are conserved between multiple species, such as human and mouse. I have tried to `liftOver`, but even though when I tweak the parameters to make it more sensitive, I lose most of my exons. To complement this approach, I am trying `blat` and it seems that is wo ...
genome alignment written 11 months ago by Geparada1.4k
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Answer: A: Converting to homologs
... I would suspect that other people have already done efforts in the gene homology direction already, as it is something that many people wants to do when you are working with more than one model organism or when you want to homologate everything to human so you can get the best usage of the available ...
written 11 months ago by Geparada1.4k
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Comment: C: How to determine if SRA file is single or paired end?
... cool! very simplified, thanks ! :) ...
written 15 months ago by Geparada1.4k
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Answer: A: Filtering sam/bam by using CIGAR deletion sites
... I would do something like: samtools view file.bam | awk '($6 ~ /D/) && ($5>10)' `($6 ~ /D/)` means "deletion in CIGAR" and `$5>10` means MAPQ>10 I really like awk oneliners for doing quick filters like this. ...
written 16 months ago by Geparada1.4k

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