User: pennakiza

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pennakiza20
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Posts by pennakiza

<prev • 15 results • page 1 of 2 • next >
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Consensus protein from aavf
... Hi all, I used a tool called HIVmmer for variant calling using HIV illumina DNA seq data. What I get back is an aavf file, which I understand is the eqivalent of a VCF for aminoacid sequence. I'd like to know if there is any way that I can get a consensus sequence of my protein read from thia file? ...
hivmmer aavf hiv written 4 days ago by pennakiza20
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Comment: C: DNA Sequencing of Single Genome Amplicons analysis
... I have 96 amplicons - I consider each one of them a different sample although they come from the same patient. I'm just a bit worried about SNP calling, as it's HIV Env and I am not sure how accurate would that be, considering the high variance in different quasi species? I'm sorry if I sound silly, ...
written 6 days ago by pennakiza20
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DNA Sequencing of Single Genome Amplicons analysis
... Hello all, I have a few DNA sequencing reads (Illumina) for HIV amplicons that are supposed to derive from single genome amplification. I have picked the samples based on the band size when run on my gel and now I'd like to confirm that my sequences are indeed coming from a single genome and that t ...
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Comment: C: Fusion sequence matching
... Hi Kevin, Thank you for your response! I have looked at almost every fusion gene detection tool out there, but unfortunately none supports long read data (like Nanopore) and therefore, I am trying to come up with alternative ideas on how to detect my fusions. Many thanks, Peny ...
written 5 months ago by pennakiza20
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Fusion sequence matching
... Hello everyone, I was wondering if it would make any sense to detect gene fusions in my RNA seq data by just matching the sequence around the fusion point to my reads. What do you think? Thank you and happy holidays! :) Peny ...
fusions rna-seq gene fusions written 5 months ago by pennakiza20
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Comment: C: Splitting long reads into shorter chunks
... Just as an example, obviously my real-life reads are huge, around 10000 nt each. However, I was planning to chunk them into pieces of 1000 nts each. ...
written 11 months ago by pennakiza20
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Comment: C: Splitting long reads into shorter chunks
... I have very long reads that I would like to pass through a fusion gene detection tool, which will not take the reads as they are, mainly because of the aligner that it uses. However, I am thinkinv of splitting them in quite large chucks (1000 bases, as opposed to the 10000 bases sequences ghat I hav ...
written 11 months ago by pennakiza20
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Splitting long reads into shorter chunks
... Hi all, I was wondering if splitting a long read to multiple ones would have any consequences on the quality of the read and I would like to read your opinions on that. Just a very simple example, say I have a 10 base sequence: @read1 ATGTGGATCA and I split it into two 5 base ones: @read1_1 ATGTG ...
long written 11 months ago by pennakiza20
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Comment: C: Fusion gene detection in sam file
... Hi Kevin, They said the same to me but in my opinion the pipeline presented in this video is not very clear. They have suggested Sniffles, Picky and NanoSV (which actually works) but these tools give me only Structural Variations - I guess users have to decide which of them are fusions and whether ...
written 11 months ago by pennakiza20
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Comment: C: Fusion gene detection in sam file
... Thank you Kevin, I have contacted them but no response yet! :( Peny ...
written 12 months ago by pennakiza20

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