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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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BWA example mapping (docs) #391

Closed keiranmraine closed 5 years ago

keiranmraine commented 5 years ago

It looks like there may be a typo in the doc page section:

https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html#reads-mapping

$ bwa mem -A1 -B4  -E50 -L0  index_path \
    -U mate_R1.fastq.gz 2>>mate_R1.log | samtools view -Shb - > mate_R1.bam

It appears that -U should be removed from the BWA command. It's not valid to have an option between index and inputs, plus -U is only relevant for paired data (and it's intentionally run as unpaired here).

joachimwolff commented 5 years ago

I think you are right, thanks for reporting.