User: mia

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mia70
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Posts by mia

<prev • 12 results • page 1 of 2 • next >
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Comment: C: getting the unmapped reads from BAM file
... Awww!!! Thanks John for clearing that up. I really appreciate that. ...
written 5 weeks ago by mia70
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Comment: C: getting the unmapped reads from BAM file
... Apologizes for that. I thought that I had hit reply. ...
written 5 weeks ago by mia70
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Comment: C: getting the unmapped reads from BAM file
... John, Thanks again for the explanation. However, I am still not getting the 22806328 + 4861610. Does this mean there a few of the passed QC reads that fail QC as well? ...
written 5 weeks ago by mia70
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Answer: A: getting the unmapped reads from BAM file
... John, The above stats are from the original SAM file BWA-meth generated. Below are the stats on the converted BAM file: 22806328 + 4861610 in total (QC-passed reads + QC-failed reads) 154024 + 1050636 secondary 0 + 0 supplementary 0 + 0 duplicates 22634029 + 4846318 mapped (9 ...
written 5 weeks ago by mia70
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Comment: A: getting the unmapped reads from BAM file
... Hi John, Yes it is from bwa-meth. I converted the sam file to bam. This sample is extracted from rust infected wheat. This means that it should contain both the rust and wheat genome. The above flagstat is after the sample was aligned to the rust genome. I am assuming that the 4861610 unmapped read ...
written 5 weeks ago by mia70
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getting the unmapped reads from BAM file
... Hi, I have SAM file after alignment and the samtools flagstat produces the following results: 22806328 + 4861610 in total (QC-passed reads + QC-failed reads) 154024 + 1050636 secondary 0 + 0 supplementary 0 + 0 duplicates 22634029 + 4846318 mapped (99.24% : 99.69%) 2265230 ...
genome bam2fastq alignment samtools written 5 weeks ago by mia70
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Comment: C: Bismark on sample with 2 genomes
... John, Downloading and installing the new version did the trick. Thanks a lot for your help. Mia ...
written 5 weeks ago by mia70
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Comment: C: Bismark on sample with 2 genomes
... John, I downloaded the bwa-meth.0.10 according to the install instructions on the github site. ...
written 5 weeks ago by mia70
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Comment: C: Bismark on sample with 2 genomes
... Hi John, I have installed bwa-meth. However, when I am trying to align the samples to I get the following error: [M::process] read 1269842 sequences (160000092 bp)... [M::process] 0 single-end sequences; 1269842 paired-end sequences [M::process] read 1269842 sequences (160000092 bp). ...
written 5 weeks ago by mia70 • updated 5 weeks ago by John11k
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Comment: C: Bismark on sample with 2 genomes
... John, I really appreciate the information you provided and I will look into BWA-meth. Also, can you provide me with the name of the workshop in Freiburg? Thanks, Mia ...
written 6 weeks ago by mia70

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