User: mia

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mia70
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Posts by mia

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Comment: C: R .libpaths issue
... Thanks Santosh!!! Sometimes you are looking at code all day and you miss the little things;) ...
written 4 weeks ago by mia70
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R .libpaths issue
... Hi, I am having am issue with my R script. At the beginning of the script I wanted to get a list of the R library paths. However, I get the following error when I run the .libpaths() command: `Error: could not find function ".libpaths"`. Has anyone come across this error before? Thanks in advance, ...
software error R written 4 weeks ago by mia70 • updated 4 weeks ago by Santosh Anand2.2k
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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 9 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 9 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 9 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 9 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 10 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 10 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 10 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 10 weeks ago by mia70

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