User: Helene

gravatar for Helene
Helene390
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390
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United States
Last seen:
2 weeks ago
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3 years, 4 months ago
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s***********@gmail.com

Posts by Helene

<prev • 102 results • page 1 of 11 • next >
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Comment: C: Difference between samtools unmapped reads and picard metrics file unmapped read
... I do not have an unmapped reads output from Picard - I do not know how to do it in Picard, I was just looking at the metrics file. That said, are you implying that in Picard, MAPQ = 0 is counted as unmapped? I think I can write a script to prove that. Thanks a lot for the reply. ...
written 5 weeks ago by Helene390
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Comment: C: Analysis of sequencing duplicates
... Thank you for the reply. I'm trying to read more about "addcount" in clumpify, but could not find it - if you are one of the authors, do you know if this command looks for perfect match among the reads, or does it allow small portion of mismatches please? ...
written 6 weeks ago by Helene390
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Comment: C: Analysis of sequencing duplicates
... Thank you very much for the reply. I'm not sure what do you mean by "name" - I thought every read has a unique name at the very start (starting with @)? ...
written 6 weeks ago by Helene390
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Comment: C: Analysis of sequencing duplicates
... Sorry I guess I was not very clear in the post. I want to count the frequency of the duplicated reads, not regions - I do not know what regions to look at yet, unless I scan through the bam file first. Thank you so much for the reply. ...
written 6 weeks ago by Helene390
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Analysis of sequencing duplicates
... I wonder if there is an existing software studies duplicates from NGS bam file. I understand that Picard and samtools can both mark/remove duplicates, but what if I want to count the frequency of each duplicated fragment? I could do some string comparison in Python and categorize the duplicates (o ...
duplicate written 6 weeks ago by Helene390 • updated 6 weeks ago by genomax40k
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Locate LOH using SNV VCF files
... I have a few WGS SNVs VCF files, generated by IVC. I wonder if there is software you would recommend to look at CNVs, mainly loss of heterozygosity (LOH) events, using these VCF files. Thank you very much. ...
snp written 8 weeks ago by Helene390
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Comment: C: Locate positions in a large bed file
... Thank you very much for the detailed information. The list of positions I'm talking about is no longer at reads level - they are just chromosome & positions. It looks like I should turn this list into another bed file, and just use "6.1.2.3.3. Retrieving elements which overlap target elements" a ...
written 3 months ago by Helene390
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Comment: C: Locate positions in a large bed file
... Thank you so much for your reply. I am looking at this too - do you happen to know how fast these two functions are for large files? ...
written 3 months ago by Helene390
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Locate positions in a large bed file
... I have a ~20G bed file for a few samples, and the bed file contains read depth for all positions of the human genome. Also, I have a list of chromosome positions (~30,000 to 50,000) for each sample, and I would like to know the read depth at these positions. What would be the most efficient method p ...
bed written 3 months ago by Helene390 • updated 3 months ago by Alex Reynolds22k
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Comment: C: Mutect 2 on WGS data takes too long to run
... I had a little experience with VarScan2 - don't you need to use samtools pileup? I recall the pileup procedure to be painfully long too... Maybe I did not do it correctly, but please comment on it. Thank you. ...
written 5 months ago by Helene390

Latest awards to Helene

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 6 weeks ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 5 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 5 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 6 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Popular Question 7 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 10 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 10 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 12 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 12 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 14 months ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
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Scholar 20 months ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
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Scholar 23 months ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

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