User: Andrew

gravatar for Andrew
Andrew50
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50
Status:
New User
Location:
Canada
Website:
http://agduncan.blogsp...
Last seen:
3 years, 7 months ago
Joined:
4 years ago
Email:
d**************@gmail.com

Posts by Andrew

<prev • 9 results • page 1 of 1 • next >
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Where can I find tumour-normal pairs public data sets
... I am looking for some public access tumour-normal pair data for a project I am working on.  Ideally this would be BAM  or VCF files, but fastq should be fine.  I've tried looking in different places like the ICGC portal and the TCGA data portal but all of the data of the file types I need are protec ...
public data tumour-normal written 3.7 years ago by Andrew50
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Batch effects in sequencing data
... I am looking for biases in sequencing data that may appear at any step in the process of sequencing, caused by batch effects.  For example, the impact of library prep on sequencing data.  I know where these biases could occur, I just don't know what type of impacts they will have (impact coverage, G ...
batch effects written 3.9 years ago by Andrew50 • updated 3.9 years ago by Thomas Johnson70
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Comment: C: Generate percent of bases with quality > x from BAM file
... This is exactly what I am looking for, thank you. ...
written 4.0 years ago by Andrew50
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Generate percent of bases with quality > x from BAM file
... I am interesting in finding the percent of bases with quality > x from a BAM file.  I want to do this multiple times for a BAM file.  So for example I might want to find percent of bases with quality > 0 and also percent of bases with quality > 50. I know I could parse data from the BAM fi ...
quality bam written 4.0 years ago by Andrew50 • updated 4.0 years ago by dariober10k
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How are expected error rates calculated?
... I want to find the overall expected error rate of reads in a BAM file, as well as the expected number of errors. Currently for each base in a read, I find the ASCII value (number) of the quality (column 11), subtract 33, and remove the phred scale, which to my understanding would give me the probab ...
expected error rate bam written 4.0 years ago by Andrew50
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Answer: A: Find reference base for a position in a given read from a BAM file
... Found the solution http://seqanswers.com/forums/showthread.php?t=17315 In case anyone finds this in the future just do the following samtools faidx <file.fa> chr1:500-500 This will get you the 500th base in the given fasta file. ...
written 4.0 years ago by Andrew50
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Find reference base for a position in a given read from a BAM file
... If I take a random read from a BAM file, and want to know what the reference base would be at position 1 of that read, is there a way to do this?  I was thinking I could do something with the POS  column of the BAM file and then add to it the position of the base in the read I am looking at to get t ...
bam written 4.0 years ago by Andrew50 • updated 4.0 years ago by Matt Shirley9.0k
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Substitution error rate and indel error rate from BAM file
... I want to determine the substitution error rate and the indel error rate for a given BAM file. I've been reading over the following article. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278762/#B1 First off I just want to confirm my definitions of a substitution error and indel error are correct. ...
substitution indel bam error rate written 4.0 years ago by Andrew50 • updated 4.0 years ago by Brian Bushnell16k
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Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
... Purely based on required header information and data/stats pulled from the BAM file, is there any way to guess the sequencing platform (454, Illumina, Ion Torrent, etc.) used to generate data for a BAM file? Does a tool already exist that does this? So far all I can find is average read lengths and ...
fastq bam written 4.1 years ago by Andrew50 • updated 3.9 years ago by Biostar ♦♦ 20

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