User: dahun73

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dahun7310
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8 months, 3 weeks ago
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Posts by dahun73

<prev • 9 results • page 1 of 1 • next >
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how to convert FASTQ to complementary sequences
... Hello All! I have two questions about fastq. Is there any possibility that FASTQ sequence is complementary for original RNA sequence? If so, how to covert fastq to complementary sequences(not reverse complementary)? Is there any useful tools..? ...
fastq alignment rna-seq written 28 days ago by dahun7310 • updated 22 days ago by Biostar ♦♦ 20
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Possibility of mapping opposite strand
... Hello All, I have question about RNA-seq data(exactly speaking, it is eCLIP-seq). For different library types, I heard FASTQ sequence is complementary with original RNAs. If so, is there any possibility of mapping opposite strand? I made a bigwig file to watch in UCSC genome browser. But some of g ...
fastq alignment star rna-seq written 29 days ago by dahun7310 • updated 29 days ago by swbarnes29.2k
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how to calculate p-value of Cuffdiff result?
... Hello All, I have a question for calculating p-value of each gene. Yes, I know that it needs at least more than 3 samples to get significant p-value. But I have one sample of each condition. it means that I have control1 and case1 samples. Then, how cuffdiff calculate this p-value of each gene? ...
p-value fpkm cuffdiff rna-seq written 3 months ago by dahun7310 • updated 3 months ago by Biostar ♦♦ 20
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how to download quality value files for csfasta in NCBI GEO datasets?
... Hello! I want to align csfasta files in GEO Datasets. Actually, I downloaded csfasta files but I couldn't find quality value files in GEO. I've known that it needs bowtie1 or tophat1 to align csfasta files. If I align the csfasta, it needs also csfasta and quality value file. Are there anyone who k ...
geo ncbi csfasta written 4 months ago by dahun7310
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eCLIP-seq peak calling using HOMER
... Hello, world! I have a question for HOMER peak calling algorithm. Homer has peak calling tools called 'findPeaks'. It has also CLIP-seq data analysis option called '-style clip'. In webpage, however, there is no information about that. Is there anyone who knows there homer CLIP-seq peak calling alg ...
clip-seq homer algorithm rna-seq peak written 4 months ago by dahun7310
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Comment: C: Filtering repetitive element during mapping
... I'm sorry for late reply. Thanks! I will check it now! ...
written 4 months ago by dahun7310
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Filtering repetitive element during mapping
... Hello, I have a question for mapping. I want to align mm10 genome without any repetitive element but it is hard to get a repetitive element sequence. RepBase is not free to use for individual user. Is there any good suggestion for mapping without repetitive element? ...
alignment mapping rna-seq written 4 months ago by dahun7310 • updated 4 months ago by JC12k
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Convert BED to BAM files
... Hello, I have question during analyzing eCLIP-seq data. Someone converted BED file to BAM file during analyzing. Can I try analyzing this BAM files? I concerned that BED are about 3GB, but BAM are just 80MB. I've known that there are many information in BAM file, and I've heard that it's not good ...
eclip clip rna-seq written 5 months ago by dahun7310
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Local installation of UCSC Genome Browser
... Hi.I have some questions for local installation of UCSC genome browser. I know that there are 5 methods of installation(https://genome.ucsc.edu/goldenPath/help/mirror.html ). But I'm poor at computer managing. So I have chosen 4th pathway(GBIC installation). https://genome.ucsc.edu/goldenpath/hel ...
genome ucsc browser written 8 months ago by dahun7310 • updated 8 months ago by RamRS30k

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