User: qyang

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qyang20
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2 years, 1 month ago
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3 years, 3 months ago
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Posts by qyang

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Comment: C: CNVkit : small CNV calling
... I would like to try the "in theory" method you mentioned to attempt to get the cnv for single exon. I understand how the 'log2' column can be used. But how the 'spread' can be used for the Z-test, can you share your ideas? ...
written 2.1 years ago by qyang20
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Is there any tool can identify which copy of chromosome reads coming from?
... Every chromosome has two copies. When reads are mapping back to the genome, the reads come from the same region of different copies could have some difference. So does the aligner or other tools can know which copy some reads coming from? ...
alignment cnv sequencing written 2.1 years ago by qyang20 • updated 2.1 years ago by Brian Bushnell16k
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Question about run cnvkit on DNAnexus
... I met a problem. I want to run the app CNVKit on DNAnexus in CLI. The command I want to execute is from the manual of CNVKit, which is cnvkit.py call Sample.cns -y -o Sample.call.cns The name of cnvkit.py on DNAnexus is cnvkit_batch So I tried: dx run cnvkit_batch call COt1049.cns -y -o COt1049. ...
cnvkit snp dnanexus written 2.2 years ago by qyang20 • updated 2.1 years ago by Eric T.2.5k
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how to determine the controls for cnv
... Among all the samples, how can we select some of them as controls for subsequent cnv? Are there criteria? ...
cnv written 2.3 years ago by qyang20 • updated 2.3 years ago by Eric T.2.5k
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Plot read counts graph on transcript only using midpoint/start position of reads or the whole read
... I would like to plot read counts graph for a transcript. I would like to use bars to represent read counts. Let's assume I have a read mapped to coordinate 100 and the length of that read is 25. My question is in the read counts graph, should I just draw a bar of height 1 at the start position 100, ...
ribo-seq rna-seq written 2.3 years ago by qyang20
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Comment: C: Could 3'-UTR have ribosomes on it?
... It's not a pure bioinformatics question, but it's closely related to bioinformatics research. ...
written 2.3 years ago by qyang20
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Comment: C: Could 3'-UTR have ribosomes on it?
... My research used Ribo-seq. I want to find out non-ribosomal RNA-protein complexes binding sites. So I would like to know whether there are ribosomes on 3'-UTR, if not, all the preserved fragment mapped to 3'-UTR should come from non-ribosomal RNA-protein complexes binding sites. That's why I have ...
written 2.3 years ago by qyang20
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(Closed) Could 3'-UTR have ribosomes on it?
... In my understanding, ribosomes will stop translation and leave mRNA when they touch stop codons. If this is correct, there should not be ribosomes on 3'-UTR. But is this correct? Are there exceptions? ...
genome written 2.3 years ago by qyang20
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Are there known nonribosomal RNA-protein complexes binding site on mRNA of arabidopsis thaliana
... Are there any dataset or paper which giving any nonribosomal RNA-protein complexes binding site on mRNA of arabidopsis thaliana? ...
rna-protein complexes arabidopsis thaliana written 3.2 years ago by qyang20 • updated 3.2 years ago by Girolamo140
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Is there a way to find out all Ribo-seq datasets for Arabidopsis thaliana in NCBI SRA
... I want to find out all available Ribo-seq datasets for Arabidopsis thaliana. But I don't find a easy or efficient way to search for these datasets. Now I just searched "arabidopsis thaliana" in NCBI SRA and checked the results one by one. I think this is not a smart way. Anyone has some suggestions? ...
ribosome profiling rna-seq written 3.3 years ago by qyang20 • updated 3.3 years ago by LLTommy1.2k

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