User: yliueagle

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yliueagle220
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France
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1 month ago
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Posts by yliueagle

<prev • 37 results • page 1 of 4 • next >
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see base quality from IGV
... A naive question, where can I see the quality of a base from IGV? When I hover the base, it does show information about it. But where can I see the quality of the base? ![enter image description here][1] [1]: https://i.ibb.co/chtT2jP/Screenshot-2020-10-22-at-17-43-23.png ...
reads igv written 5 weeks ago by yliueagle220 • updated 5 weeks ago by ATpoint42k
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Comment: C: many read aligned to the same position but with different variants
... Thanks for your answer. Here I updated the figure. These reads mapped exactly to the same region except that they have different variants, especially at the position near 60795540 ...
written 5 weeks ago by yliueagle220
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many read aligned to the same position but with different variants
... (Please open this link if image not displayed: https://ibb.co/mHYH8NC I have two questions related to the following alignment from a single sequencing sample of a cell line: (1) are the reads in the bottom represent PCR duplicates, as they are aligned exactly to the same position (2) if they are d ...
reads duplicates alignment written 5 weeks ago by yliueagle220 • updated 5 weeks ago by genomax92k
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bowtie2 inpipe1 inpipe2
... I used the following bowtie script to do the alignment: bowtie2 -x ./hg19 -p 22 -1 my_R1_001.fastq.gz -2 my_R2_001.fastq.gz -S out.sam however, in the out.sam header it looks like this: @PG ID:bowtie2 PN:bowtie2 VN:2.2.9 CL:"xx/3.Software_packages/bowtie2-2.2.9/bowtie ...
bowtie2 written 3 months ago by yliueagle220 • updated 3 months ago by _r_am31k
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Answer: A: Extract base information from aligned reads in a sam file
... I found http://lindenb.github.io/jvarkit/Sam2Tsv.html can do the job. Thanks all! ...
written 3 months ago by yliueagle220
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Comment: C: Extract base information from aligned reads in a sam file
... Thank you. This do obtain the reads but I also need to retrieve the basepair information from reads.sam at chr:start-end ...
written 3 months ago by yliueagle220
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Comment: C: Extract base information from aligned reads in a sam file
... Not only counts, but the basepair at that position for each read, with read name included in the output. (Of course the counts can be generated from this table as a downstream step) ...
written 3 months ago by yliueagle220
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Extract base information from aligned reads in a sam file
... I generated a sam (bam) file by aligning fastq to reference using BWA. Now I would like to retrieve the the basepair at a given chromosome position, for example, chr12:11010100:11010100, for all reads aligned to this region, how can I do that? Thanks! (My expected workflow would be: (1) extract read ...
reads basepair sam written 3 months ago by yliueagle220
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Can not change track height of IGV
... I am using IGV v2.8.0 on mac. I wanted to display multiple similar data tracks in the .bed format. As have many of them, I would reduce the track height so that I can see all of them without scrolling the window. The default track height is 40. I can only increase the track height but not to reduce ...
igv written 9 months ago by yliueagle220
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Intron and exon coordinates of all genes from Hg19
... Is there a way to get Intron and exon coordinates of all genes from Hg19? The exons can be got from this post: https://www.biostars.org/p/6391/, but how can I also get intron coordinates? I would keep the corresponding gene names in the result Thanks! ...
gene cordinates intron exon written 11 months ago by yliueagle220 • updated 11 months ago by vkkodali2.2k

Latest awards to yliueagle

Scholar 3 months ago, created an answer that has been accepted. For A: Extract base information from aligned reads in a sam file
Popular Question 14 months ago, created a question with more than 1,000 views. For Why low MAF leads to low power
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Why low MAF leads to low power
Great Question 3.7 years ago, created a question with more than 5,000 views. For DAVID: functional annotation chart result explanation
Great Question 3.7 years ago, created a question with more than 5,000 views. For Map gene name to gene ID
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Why low MAF leads to low power
Popular Question 3.7 years ago, created a question with more than 1,000 views. For DAVID: functional annotation chart result explanation
Popular Question 3.7 years ago, created a question with more than 1,000 views. For GWAS dataset: SNPs with association p-value
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How to group genes as 'gene sets'
Popular Question 4.1 years ago, created a question with more than 1,000 views. For DAVID: functional annotation chart result explanation
Popular Question 4.1 years ago, created a question with more than 1,000 views. For GWAS: low explained heritability
Student 4.1 years ago, asked a question with at least 3 up-votes. For Why do genes have so many synonyms?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For GWAS dataset: SNPs with association p-value
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Why do genes have so many synonyms?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Why do genes have so many synonyms?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For GWAS dataset: SNPs with association p-value
Appreciated 4.9 years ago, created a post with more than 5 votes. For gene (or SNP) related to a disease
Good Question 4.9 years ago, asked a question that was upvoted at least 5 times. For gene (or SNP) related to a disease
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Why do genes have so many synonyms?
Student 5.9 years ago, asked a question with at least 3 up-votes. For Why do genes have so many synonyms?
Good Question 6.1 years ago, asked a question that was upvoted at least 5 times. For Why do genes have so many synonyms?
Appreciated 6.1 years ago, created a post with more than 5 votes. For Why do genes have so many synonyms?
Student 6.1 years ago, asked a question with at least 3 up-votes. For Why do genes have so many synonyms?

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