User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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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 16 days ago by bioinforesearchquestions150
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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 17 days ago by bioinforesearchquestions150 • updated 17 days ago by gconcepc20
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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 4 weeks ago by bioinforesearchquestions150 • updated 9 days 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 7 weeks ago by bioinforesearchquestions150
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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 8 weeks ago by bioinforesearchquestions150 • updated 8 weeks ago by WouterDeCoster31k
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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 4 months ago by bioinforesearchquestions150
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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 4 months ago by bioinforesearchquestions150
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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 4 months ago by bioinforesearchquestions150
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Comment: C: How to anntate small-RNA seq reads distribution
... Hi, I am planning to do the same requirement as yours. Annotate the percent of reads with miRNA, snoRNA, rRNA, tRNA and repeat for sequenced reads from pig. Would you provide any recommendations? ...
written 4 months ago by bioinforesearchquestions150
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how to annotate (rRNA, tRNA, Mt_rRNA, Mt_tRNA, etc) sequenced small RNA reads
... Hi, I have small RNA sequenced data. I annotated the small RNA sequenced reads against miRBase for miRNAs. I would like to annotate the sequenced small RNA reads into the following mRNA_coding_sequence rRNA tRNA mRNA_1000 TSS + 5UTR mRNA_3UTR Mt_rRNA Mt_tRNA misc_RNA piRNA snRNA snoRNA ...
annotation small rna rna-seq written 4 months ago by bioinforesearchquestions150

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