User: mglasena

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mglasena0
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Posts by mglasena

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Comment: C: BWA-MEM - Improperly Paired Reads
... I found the source of my issue. The data I've downloaded from NCBI is supposed to be paired-end reads of 100 bp length. However, the forward and reverse reads are identical, which must have been a mistake during NBCI SRA submission. Am I just out of luck at this point? Or should I contact the resear ...
written 15 days ago by mglasena0
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Comment: C: BWA-MEM - Improperly Paired Reads
... I appreciate the tips. I'm just getting started with genome analysis. ...
written 26 days ago by mglasena0
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Comment: C: BWA-MEM - Improperly Paired Reads
... Picard MarkIlluminaAdapters adds the XT tag to a read record to mark the 5' start position of the specified adapter sequence. Picard SamToFastq changes the quality scores of bases marked with an XT tag to two, which should effectively prevent the adapter portion from contributing to read alignment a ...
written 26 days ago by mglasena0
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BWA-MEM - Improperly Paired Reads
... After aligning paired-end 100bp reads to a reference genome, I am getting very low properly paired percentage: 369208441 0 total (QC-passed reads + QC-failed reads) 8985531 0 secondary 289733341 0 mapped 78.47% N/A mapped % 360222910 0 paired in sequencing ...
genome gatk next-gen alignment bwa written 26 days ago by mglasena0 • updated 26 days ago by genomax91k

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