Only R1 reads mapped for paired-end read input?

[Yuqia]

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]

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]

Many thanks Sina! Best, Yuqia