pair-map using bowtie2 by --mapper failed

[hao-yanan]

Hi!

I failed to do bowtie2 pair-map with --mapper bowtie2 setting. This is my command, has some problems. Could you give me some suggestion about how to do pair mapping? Many thanks!

tadbit map --mapper bowtie2 --renz MboI -w sample1
--index /home/database/yeast
--fastq SRR4433970_1.fastq --read 1
--fastq2 SRR4433970_2.fastq --read 2

[david-castillo]

Hello,

Can you post the error message that you are having?

Regards

David