User: jsw940

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jsw94010
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Posts by jsw940

<prev • 7 results • page 1 of 1 • next >
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Plots for gene expression data
... Hello. I have a question about plots which represent RNA-sequencing results. I have two RNA-sequencing data. One is from gene 'A' knock-down and the other is gene 'B' knock-down. And I found some genes which was up-regulated when 'A' was knocked-down and at the same time down-regulated when 'B' was ...
genome R rna-seq written 16 days ago by jsw94010
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Detection T cell receptor transcripts
... Hello, I planned to explore diverse T cell receptor transcripts using long-read sequencing. So I transfected TCR mini gene into cells and got sequencing data. I mapped my data to genome reference and visualize it via IGV. But I couldn't see any transcripts from TCR plasmid on the chromosome 7 where ...
sequence next-gen rna-seq written 23 days ago by jsw94010
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PTC positions in transcripts
... Hello, I have a question about Ensembl genome data. There are lots of transcripts annotated as "nonsense_mediated_decay" in ensembl data. Then, I think that PTC(premature termination codon) must be in that transcript. So, how can I know the position and kinds of PTC which is the evidence of annota ...
rna-seq sequencing written 6 months ago by jsw94010 • updated 6 months ago by i.sudbery8.4k
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Sorting unannotated transcripts
... Hi, now I'm studying how to handle RNA sequencing result. I have a question about "annotation". I made transcriptome using stringtie(with GTF annotation file) and analyze splicing patterns with GFFcompare. My aim is compare splicing patterns between normal condition and knock down condition trans ...
rna-seq written 6 months ago by jsw94010
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Comment: C: What is a better strategy for finding novel transcripts?
... Thank you very much! Now I'm following your guidelines. But my raw data was not mapped with STAR(it said that my read is too short! so I'm adjusting some parameters.), Instead, I used minimap2 and stringtie2. And finally I could visualize my data and check my transcripts. Your mention is so helpful ...
written 6 months ago by jsw94010
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Comment: C: What is a better strategy for finding novel transcripts?
... Yes, I used minimap2 with GRCh38.p13.genome. Honestly, I have difficulty to choose reference genome and annotation. How can I choose genome version compatible with my analyze plan? Until now, I followed genome version used in papers. ...
written 6 months ago by jsw94010
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What is a better strategy for finding novel transcripts?
... Hi, I've started learning RNA-seq only recently. I use nanopore technology(cDNA sequencing) for finding novel transcripts. But I don't know exactly which analyze tools are suit for this. I read several papers about this but I couldn't fully understand. For example, I wanted to visualize my sequenci ...
rna-seq sequencing written 6 months ago by jsw94010 • updated 6 months ago by Amitm1.9k

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