User: jianzheng934963534

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Posts by jianzheng934963534

<prev • 15 results • page 1 of 2 • next >
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How samtools calculate error rate
... I have aligned the fastq file to the reference genome and got a sam file. I know use "samtools stats" can get "error rate" of the sam file. Is there any document shows how the error rate is calculated from the sam file? (since I want to seperately calculate the error rate of every read in the sam f ...
samtools sequencing written 9 weeks ago by jianzheng9349635340 • updated 9 weeks ago by Devon Ryan71k
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Count error rate of sam file
... Hi I have aligned the fastq file to the reference genome and got a sam file. I know use "samtools stats" can get "error rate" of the sam file. Is there any document shows how the error rate is calculated from the sam file? (since I want to seperately calculate the error rate of every read in the sa ...
sequence next-gen alignment samtools written 10 weeks ago by jianzheng9349635340 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: The difference between sam files
... I know how to simply achieve this but I want to find a fast way because the sam file can be huge. ...
written 11 weeks ago by jianzheng9349635340
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Comment: A: The difference between sam files
... more simply. I want to know how to extract the CIGAR flags of the same readID from two different sam files. Thanks. ...
written 11 weeks ago by jianzheng9349635340
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(Closed) Compare two sam files
... Hi all! last time I post my question but get no perfect answer. So this time I decide to describe my question more simply. So I want to know how to extract the CIGAR flags of the same readID from two different sam files. Thanks. ...
genome samtools sam sequencing written 11 weeks ago by jianzheng9349635340
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Comment: C: The difference between sam files
... Thanks for your answer. To be more specific,first,I have an fastq file and I align it to the reference genome and get 1.sam, then I deal with some of the reads in the fastq file and align it to the reference genome again and get 2.sam, and now I want to compare the CIGAR flags of the reads with the ...
written 11 weeks ago by jianzheng9349635340
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The difference between sam files
... Hi all! I want to compare the result of alignment of reads that has the same name in two .sam files, especially the difference in CIGAR flags. Is there any fast way to implement? ...
alignment samtools sam sequencing written 11 weeks ago by jianzheng9349635340
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(Closed) pacbio data filter
... Hi all. I have an fastq file of pacbio data. Now I want to filter out all the reads with length less than 100bp in the fastq file, is there any easy and efficient way? thanks. ...
tgs filter fastq pacbio sequencing written 12 weeks ago by jianzheng9349635340
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Comment: C: coverage of fastq file
... I mean that in some papers they mention the file is 20x, by calculating I get 18.75, so how do they get that the fastq file is 20x? ...
written 3 months ago by jianzheng9349635340
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Comment: C: coverage of fastq file
... The main problem is that those papers give the coverage as an integer(such as 20x) but by calculating I can only get a float number, not exactly, if it is 18.75(for example), I can guess that the coverage may be 20x. So I think there is informaion about the coverage of the fastq read(through ncbi) B ...
written 3 months ago by jianzheng9349635340

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