User: nilshomer

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nilshomer60
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Posts by nilshomer

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Answer: A: fgbio: Calling consensus reads using UMI
... The answer is in the source code of the [SingleStrandUmiSomaticVariantCalling][1] pipeline, which references the following [task in dagr][2], which was linked in the original blog post. The main idea is to create the unmapped BAM, feed the unmapped BAM into `SamToFastq`, stream the output of `SamTo ...
written 18 months ago by nilshomer60
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Comment: C: Bwa Alignments With Gaps
... There are three alignment algorithms within bwa. Do you mean "bwa aln" (backtrack), "bwa bwasw" (bwa smith-waterman), or "bwa mem" (maximal-exact-matching)? I assume the first since you are talking about "maximum mismatches". I would suggest reading Heng Li's original BWA paper and post specific ...
written 5.9 years ago by nilshomer60
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Answer: A: Picard Library: H And B Types
... You could convert the file from BAM to SAM, then use your favorite language to remove the offending tags from each line (sed, awk, perl, python, and even Samtools only C library), and then finally convert back to BAM. The rest is left as an exercise to the reader. ...
written 5.9 years ago by nilshomer60
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Answer: A: Extract Reads In Fastq Using A Bed File.
... A fastq file does not contain coordinate information. First, you must map/align the data to your reference genome (say with bwa), and then you can extract the sequences/reads using the coordinates in the BED file. ...
written 6.0 years ago by nilshomer60

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Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Extract Reads In Fastq Using A Bed File.

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