Hello, I am trying to use Megahit to assemble my Illumina HiSeq reads. Here is the Megahit parameter:
./megahit [options] {-1 <pe_1.fq> -2 <pe_2.fq> | --12 <pe12.fq> | -r <se.fq>}
```
`-1/-2`, `--12` and `-r` are parameters for inputting paired-end, interleaved-paired-end and single-end files. They accept files in fasta (*.fasta*, *.fa*, *.fna*) or fastq (*.fastq*, *.fq*) formats. They also supports gzip files (with *.gz* extensions) and bzip2 files (with *.bz2* extensions). Please run `./megahit -h` for detailed usage message.
What does "interleaved-paried-end" file mean? I have joined my R1 and R2 fastq file into one file because they have overlaps. I am not sure if I should use "--12" (for interleaved) or "-r" parameter (for single end files)
Thanks
./megahit [options] {-1 <pe_1.fq> -2 <pe_2.fq> | --12 <pe12.fq> | -r <se.fq>}
```
`-1/-2`, `--12` and `-r` are parameters for inputting paired-end, interleaved-paired-end and single-end files. They accept files in fasta (*.fasta*, *.fa*, *.fna*) or fastq (*.fastq*, *.fq*) formats. They also supports gzip files (with *.gz* extensions) and bzip2 files (with *.bz2* extensions). Please run `./megahit -h` for detailed usage message.
What does "interleaved-paried-end" file mean? I have joined my R1 and R2 fastq file into one file because they have overlaps. I am not sure if I should use "--12" (for interleaved) or "-r" parameter (for single end files)
Thanks
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