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DessimozLab / read2tree

a tool for inferring species tree from sequencing reads
MIT License
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Only R1 reads mapped for paired-end read input? #50

Closed Yuqia closed 10 months ago

Yuqia commented 10 months ago

Hello,

I input 2 paired-end read files for the --reads option, separated by a space, but only the name of the R1 reads were shown in the mplog.log file and in all output files/folders.

Does this mean that only R1 reads were mapped?

Do I need to use the option _--check_matepairing in order for both R1 and R2 reads are used in mapping?

Thank you very much! Best, Yuqia

sinamajidian commented 10 months ago

Hi Yuqia Both of the reads (R1 and R2) are being used. That's only the naming and no other option is needed. Using --debug option you can see the exact command line that is run using aligner.
Best regards, Sina

Yuqia commented 10 months ago

Many thanks Sina! Best, Yuqia