User: yancychy

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yancychy10
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2 years, 12 months ago
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Posts by yancychy

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Why 3'-UTR length is 1 or 0?
... Thanks very much. The real 3'UTR length is 57531792 - 57531782 + (57532426 - 57532281) = 155. Thanks for the explaination of non-coding RNA and the UTR length. It's very clear. ...
written 6 weeks ago by yancychy10
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Why 3'-UTR length is 1 or 0?
... Hi, I want to get the 5'-UTR and 3'-UTR coodinates from the annotation file. I downloaded the "All GENCODE VM24" bed file from UCSC genome browser. The format of the bed file is following: bin name chrom strand txStart txEnd 1023 ENSMUST00000000090 ...
genome gene sequence written 6 weeks ago by yancychy10 • updated 6 weeks ago by i.sudbery7.3k
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Comment: C: Build repeat genome index using STAR
... Yes. Thanks very much ...
written 4 months ago by yancychy10
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Comment: C: Build repeat genome index using STAR
... Thanks. I tired to limit STAR to 40gb. The error is same. I think the problem may caused by the input files. repeatSeq.fa >hg38_rmsk_L1P5 range=chr1:67108754-67109046 5'pad=0 3'pad=0 strand=+ repeatMasking=none AACAAATAATCCCATCAAAAAGTAGGCAAAGGATATGAATAGATAATTTT CAAAATAAGATATACAAATG ...
written 4 months ago by yancychy10 • updated 4 months ago by h.mon29k
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Comment: A: Build repeat genome index using STAR
... Thanks. I tired the --limitGenomeGenerateRAM. It produced same error. ...
written 4 months ago by yancychy10
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Build repeat genome index using STAR
... Hi , I downloaded the repeat genome and gtf (RepeatMasker) files from UCSC genome table browser. I want to build repeat genome index to remove the reads which may be spurious artifacts from rRNA (& other) repetitive reads. But the error is always exceeding memory limit. I adjust the memory ...
repeat star index written 4 months ago by yancychy10
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Answer: A: How to validate the Gene connections?
... Thank you so much. Petr and badribio, I will try use the databases, Many thanks. ...
written 2.9 years ago by yancychy10
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How to validate the Gene connections?
... Hello, I have built a connection networks of several genes. But I don not know how to validate the correlation between these genes? Is there any gene networks databases which can help me to validate my networks? Many thanks. Best regards, ...
gene genome written 2.9 years ago by yancychy10
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Comment: C: how to get the full mRNA from the coordinate of DNA and transcript id
... I want to get the corresponding RNA sequence for the short position information ...
written 2.9 years ago by yancychy10
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Comment: C: how to get the full mRNA from the coordinate of DNA and transcript id
... Thank you very much. I will try it. I hope I can download the tools and files into local PC, and run the tools to process the bed files ...
written 3.0 years ago by yancychy10

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