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low mapping percentage in bwa mem

Just answering, following extensive back and forth in the comments. I think that your reads are fine: FASTQC doesn't see anything too weird. You see some noise at the first few basecalls but I am not ...
Maximilian Press's user avatar
1 vote

what does 8 stands for in bwa mem command line

When you have questions on software then the first thing is to do your due diligence and read the manual: https://bio-bwa.sourceforge.net/bwa.shtml Then simply checking for the "-t" argument ...
ATpoint's user avatar
  • 1,420
1 vote

Reference genome (bwa -mem)

What you need is the genome sequence in fasta format, typically suffixed .fa, for example from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/ This ...
ATpoint's user avatar
  • 1,420
1 vote

How fo force nextflow to repeat a process until all values in a particular channels are used up BUT a single value from another channel is needed

Use a value channel: exampleChannel_onething = Channel.value(1) On existing channels, you can use https://www.nextflow.io/docs/latest/operator.html#first (or ...
Rolf's user avatar
  • 111

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