User: joseludenia

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Posts by joseludenia

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Comment: C: Interpreting detected "duplicates" between different tools
... There are not overrepresented reads in Fastq results and there are 0 optical duplicates in Markduplicates. Is it possible that MarkDuplicates only take into account the 5' coordinate of the reads to decide if they are duplicated and for this reason reads that were not considered duplicated in Fastq ...
written 19 days ago by joseludenia0
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Comment: C: Interpreting detected "duplicates" between different tools
... I know that FastQC only analyzes the first 100.000 reads and mark duplicate only considers mapped reads. But I only have 30.000 reads, therefore all the readings are taken into account. On the other hand all the readings are mapped. Why in this case both tools do not consider the same data? I think ...
written 20 days ago by joseludenia0
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Answer: A: Interpreting detected "duplicates" between different tools
... I have a Fastq file with 30,000 reads (less than 100.000). When I analyze them with Fastqc the level of duplicates goes very high. Then I trim the readings to eliminate low quality bases and the levels of duplicates drop to normal levels. I suppose this will be because when I change the length of th ...
written 20 days ago by joseludenia0
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(Closed) Problem with Percent duplication on MARK DUPLICATES
... Hello. I have a Fastq file with 30,000 reads. When I analyze them with Fastqc the level of duplicates goes very high. Then I trim the readings to eliminate low quality bases and the levels of duplicates drop to normal levels. I suppose this will be because when I change the length of the readings th ...
galaxy duplicates optical sequence-read written 21 days ago by joseludenia0 • updated 21 days ago by Jennifer Hillman Jackson25k
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Comment: C: Interpreting detected "duplicates" between different tools
... Thank you very much. ...
written 23 days ago by joseludenia0
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Interpreting detected "duplicates" between different tools
... Hello. When I analize my data in FASTQC, the SEQUENCE DUPLICATION LEVELS are ok (green lavel and percent of seqs remaininig if deduplicated 75%). Then a use MAP WITH BWA to aling the reads and I get the BAM file. But when I perform MARK DUPLICATES with the BAM file, the PERCENT_DUPLICATION is 0.82, ...
galaxy samtools fastqc bwa picard written 24 days ago by joseludenia0

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