User: younglin113

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younglin11340
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Posts by younglin113

<prev • 26 results • page 1 of 3 • next >
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How to deal with the twice BS-seq data for the same sample?
... Hello everyone, Recently, I am dealing with a batch of BS-seq based single-base resolution DNA methylation data. But I got into this trouble: for the same sample, since the sequencing depth was not enough in the first time, so we added another sequencing procedure. And now I want to analy ...
dna methylation bs-seq written 12 weeks ago by younglin11340
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Using PLINK to join SNPs based on HapMap release 23
... I recently read an article about SNPs analysis. And I cannot find out how they did the process. Here is the description in this article: INRICH was used to infer the relationship between H4K16ac changes and PLINK-joined AD GWAS SNP intervals (linkage due to HapMap release 23) using standard paramet ...
plink;snp written 3 months ago by younglin11340 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: The confused result of samtools sort
... Thanks a lot. It's really helped my doubts. ...
written 11 months ago by younglin11340
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Comment: C: The confused result of samtools sort
... Oh, so it is. Thanks a lot. So I just need to change the header and it can sort as I want it to, is that what you mean ? ...
written 11 months ago by younglin11340
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The confused result of samtools sort
... Recently, I was doing an RNA-seq project, and I used spike-in control sequences in my experiment. So I mapped the reads to both human genome and spike-in sequences. And I successfully got the bam file, but when I tried to use the command `samtools sort -o aa_sorted.bam aa.bam` to sort the bam file a ...
software error alignment rna-seq written 11 months ago by younglin11340 • updated 11 months ago by finswimmer13k
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Comment: C: About the ERCC spike-in sequence reads quantification
... Yes, the bam file contains the GLuc and CLuc sequences. And the two genes in my gtf file is not the same. They are "GLuc" and "CLuc", just look similar in this picture. And the bam file shows like this : ![enter image description here][1] [1]: https://i.ibb.co/cLQC17X/TIM-20190322213501.png ...
written 11 months ago by younglin11340
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Comment: C: About the ERCC spike-in sequence reads quantification
... Because the spike-in sequences I used is not exactly the Thermofisher version. And the gtf file I made up seems really normal, right? ...
written 11 months ago by younglin11340
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About the ERCC spike-in sequence reads quantification
... Here is the situation: I want to count the reads number of spike-in sequences of an RNA-seq project. And I already mapped the reads to both the human genome and spike-in sequences, and got the bam files. Then I tried to use featurecounts tool to quantify the reads number of both genes and spike-in s ...
genome gene next-gen rna-seq sequencing written 11 months ago by younglin11340 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: low unique mapping ratio of RNA-seq data
... I tried the `samtools view -F 256` command, and the number of rows of the output file equals the clean reads number. So this command actually only output the multiple mapping reads for once, rather than filter out those multiple mapping reads, doesn't it? And here is the exact number of a sample: cl ...
written 11 months ago by younglin11340
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Comment: C: low unique mapping ratio of RNA-seq data
... The overrepresented sequences are :![enter image description here][1] [1]: https://i.ibb.co/dmfMDrD/image.png And I filtered the unique mapping reads use command: `samtools view -q 20` , the reads with mapping quality lower than 20 were determined as multiple mapping reads. ...
written 11 months ago by younglin11340

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Popular Question 9 months ago, created a question with more than 1,000 views. For I got some diffculties when run rMATs

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