Allowed base mismatches

[AgustinPardo]

Hello,

I would like to know how can I change the allowed base mismatches (-m flag). I have tried these commands, but it seems not to be working:

$ ./idemp -b ../Primavera_2014/barcode_sample.txt -I1 ../Primavera_2014/I1_SAM117-126_S3_L001_R1_001.fastq -R1 ../Primavera_2014/SAM117-126_S3_L001_R1_001.fastq -R2 ../Primavera_2014/SAM117-126_S3_L001_R2_001.fastq -m n=2 -o ../Primavera_2014/Idemp_out2

$ ./idemp -b ../Primavera_2014/barcode_sample.txt -I1 ../Primavera_2014/I1_SAM117-126_S3_L001_R1_001.fastq -R1 ../Primavera_2014/SAM117-126_S3_L001_R1_001.fastq -R2 ../Primavera_2014/SAM117-126_S3_L001_R2_001.fastq -m 2 -o ../Primavera_2014/Idemp_out2

Thanks

[yhwu]

Just -m 2 . Your input looks like for hiseq. I am not sure it will work. It was developed for miseq.

…

On Tue, May 8, 2018 at 3:28 PM, Agustin Pardo ***@***.***> wrote: Hello, I would like to know how can I change the allowed base mismatches (-m flag). I have tried these commands, but it seems not to be working: $ ./idemp -b ../Primavera_2014/barcode_sample.txt -I1 ../Primavera_2014/I1_SAM117-126_S3_L001_R1_001.fastq -R1 ../Primavera_2014/SAM117-126_S3_L001_R1_001.fastq -R2 ../Primavera_2014/SAM117-126_S3_L001_R2_001.fastq -m n=2 -o ../Primavera_2014/Idemp_out2 $ ./idemp -b ../Primavera_2014/barcode_sample.txt -I1 ../Primavera_2014/I1_SAM117-126_S3_L001_R1_001.fastq -R1 ../Primavera_2014/SAM117-126_S3_L001_R1_001.fastq -R2 ../Primavera_2014/SAM117-126_S3_L001_R2_001.fastq -m 2 -o ../Primavera_2014/Idemp_out2 Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADCfAJcXYi0f5JEPB4N5AHqNac0c1VzKks5twfHigaJpZM4T3NU3> .