bowtie mate 2 error

Question

[Morris_Chair]

Hello everyone,

I'm working on ChIP-seq files and I'm getting this type of error

mem: invalid option -- '2'

here is the code :

bwa mem hg38.fa -1 R1_001.fastq.gz -2 R2_001.fastq.gz | samtools sort > file.bam

I'm working on paired end ChIP-seq experiment so I have to use both files, I'm new to it so I wonder also if I have to unzip first ,

thank you for you support

[Arup Ghosh]

The current version of bwa mem does not have any -1 or -2 option.

bwa mem [options] <idxbase> <in1.fq> [in2.fq]

Answer 1

[h.mon]

You are mixing up bowtie2 and bwa mem: you are calling bwa mem, but -1 and -2 are bowtie / bowtie2 arguments.