User: m.hummel

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m.hummel10
Reputation:
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New User
Location:
Germany
Last seen:
1 year, 3 months ago
Joined:
4 years, 2 months ago
Email:
m*******@dkfz.de

Posts by m.hummel

<prev • 5 results • page 1 of 1 • next >
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Answer: A: TEQC - new version Bioc - problem with IRanges
... Thank you for pointing this out. The problem is most probably related to chromosomes in the bam file without any mapped reads. I have changed get.reads() in order to remove those chromosomes (seqlevels) from the resulting GRanges object. This fix should be available soon in the development version o ...
written 15 months ago by m.hummel10
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Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... TEQC reads bam files with the 'scanBam' function in the 'Rsamtools' package. This function uses 'scanBamFlag' to determine which reads to keep based on the FLAG field in the bam file (second column). Secondary alignments have flag = 256, and filtering those out with 'scanBam' should be equivalent t ...
written 2.2 years ago by m.hummel10
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Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... That only primary alignments are kept in 'get.reads' was introduced in TEQC version 3.13.1. If the error still appears for recent TEQC versions and/or after removing secondary alignments from the bam, I should have a closer look. Manuela ...
written 2.2 years ago by m.hummel10
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Answer: A: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... Hi Tommy, yes, each ID should be there twice (or only once, if the mate could not be mapped). The error occurs if there are IDs that appear more than 2 times, e.g. when there multi-mapping reads. When reading a bam file with 'get.reads', automatically only primary alignments should be kept. But ma ...
written 2.2 years ago by m.hummel10
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Job: (Bio-)Statistician at dkfz, Heidelberg, Germany
... The Division of Biostatistics is seeking a (Bio-)Statistician (Ref-No. 285/2016)   Description: The German Cancer Research Center (DKFZ) is the largest biomedical research institute in Germany with the task to systematically explore the mechanisms of carcinogenesis and identify cancer risk facto ...
job biostatistics germany written 2.9 years ago by m.hummel10

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