User: dina91n

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dina91n0
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Posts by dina91n

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Comment: C: PCR duplicate reads - samtools
... Thank you for your hint! I have two questions: 1) I used the following command to filter out secondary alignments and to get the number of reads aligned (number of lines in the file) : samtools view -h -F 256 file.bam > primaryAlign.bam grep -v '^@' primary_align.bam | wc -l the numbe ...
written 5 weeks ago by dina91n0
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Comment: C: PCR duplicate reads - samtools
... Thank you for your answer. Therefore, should I filter the secondary alignments to get the real number of duplicate reads? How can I do this? Is there a faster way to get the number of duplicate reads? Thank you in Advance! ...
written 6 weeks ago by dina91n0
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PCR duplicate reads - samtools
... Dear All, I am trying to find the PCR duplicate reads from the bam/sam. I have used picard to mark duplicates in the bam/sam file and then samtools flagstats. I obtained the following output: 196499952 + 0 in total (QC-passed reads + QC-failed reads) 125920476 + 0 secondary 0 + 0 suppl ...
flagstats duplicated picard samtools written 6 weeks ago by dina91n0 • updated 6 weeks ago by swbarnes27.5k

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