User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Comment: C: Error in cummeRbund R library package (Error: Columns index not found)
... Yeah, tried without that as well. Same error and empty cuffset instance. ...
written 16 days ago by bioinforesearchquestions180
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Error in cummeRbund R library package (Error: Columns index not found)
... Hi, With the below cuffdiff output, I already generated plots using cummeRbund package. But now, I am getting some error. What could be the reason? Have anyone faced it before? cuff_data <- readCufflinks("/Users/admin/Desktop/RNA_seq_Analysis/cuffdiff", rebuild = T) Creating databa ...
rnaseq cummerbund cuffdiff written 17 days ago by bioinforesearchquestions180 • updated 17 days ago by genomax57k
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Comment: C: What is the appropriate assembler for PacBio long reads
... As of now, I have been told that I am going to get only the PacBio long reads. Why do you say that I should get some Illumina? ...
written 11 weeks ago by bioinforesearchquestions180
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What is the appropriate assembler for PacBio long reads
... Hi folks, We got long reads sequenced from 10 bacteria using Pac Bio sequencing platform. 5 of them don't have reference bacterial strains and 5 of them have some bacterial strain closer to the subject. I have to identify anti microbial resistant genes from these 10 bacteria. This is the first tim ...
assembly alignment written 11 weeks ago by bioinforesearchquestions180 • updated 11 weeks ago by gconcepcion20
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how to evaluate coverage at a regions of interest and generate specificity, sensitivity and PPV for that region?
... Hi guys, We have exome sequenced samples at a minimum of 15X coverage using capture kits. - We would like to * identify genes that may have low coverage because no probes are available * identify gene that falls within a region which is difficult to sequence by the capture kit - how to ev ...
dnaseq specificity sensitivity snp ppv written 3 months ago by bioinforesearchquestions180 • updated 10 weeks ago by Biostar ♦♦ 20
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Are there any tools for comparing structural variants between different callers?
... Hi Folks, Are there any tools for comparing structural variants between different callers (Manta/Snowman/Delly/Lumpy)? ...
structural variants sv written 3 months ago by bioinforesearchquestions180
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How to align the sanger sequenced fragments against human reference gene?
... Hi folks, I have been provided sequence file from Sanger sequencing platform. It has 12 exons, so the technician has captured 5'UTR+exon1, exon2, exon3,.......exon12+3'UTR. He asked me to align with the human reference gene and try to find the variants from it. He provided me many fragments of sequ ...
dnaseq alignment align sanger written 4 months ago by bioinforesearchquestions180 • updated 4 months ago by WouterDeCoster32k
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While generating the % of mapped reads to all miRNAs, do I need to consider unique or multi-match reads?
... Hi folks, I am trying to create a table for the distribution of mapped RNA sequenced reads across miRBase v.21 for each isomiRs. I am using contents from this **miRBase.mrd** file to generate the reads mapped to isomiRs. I have copied the sample output from **miRBase.mrd** file generated using m ...
rnaseq mirdeep2 mirna written 6 months ago by bioinforesearchquestions180
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Comment: C: Need help in selecting the correct output file from miRDeep2?
... Thanks, I have made changes to the existing post itself. ...
written 6 months ago by bioinforesearchquestions180
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Comment: C: Need help in selecting the correct output file from miRDeep2?
... Hi Michael, I am going to delete the old one and retain the new one. ...
written 6 months ago by bioinforesearchquestions180

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