User: pennakiza

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pennakiza20
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Posts by pennakiza

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Filter out low coverage and minor alleles of a frequency above 40%.
... So, I've got a vcf file of a single genome (HIV provirus) and what I would like to do is to confirm that there is only one genome indeed, by checking if there are any accurate variants. In this context, I thought that if I get rid of any rows of low coverage variants and minor alleles that appear le ...
written 11 weeks ago by pennakiza20 • updated 11 weeks ago by finswimmer12k
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Filter out low coverage and minor alleles of a frequency above 40%.
... Hello, I was wondering if there is anybody to help me filter my vcf file (from freebayes) in order to check for heterogeneity in my single genome sequencing data. I assume I should use: vcftools --vcf my.vcf --maf 0.4 --recode --recode-INFO-all --out my_filtered.vcf but I am not sure how I ...
vcf variant calling freebayes hiv written 11 weeks ago by pennakiza20 • updated 10 weeks ago by bari.ballew190
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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 3 months 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 3 months ago by pennakiza20
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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 8 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 9 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 14 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 14 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 14 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 14 months ago by pennakiza20

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