Question: Can we map fastq files with paired ends using bwa mem on galaxy?
0
gravatar for mychung
12 days ago by
mychung0
Taiwan
mychung0 wrote:

I have a collection of timmed fastq files from WES, each contain paired ends. Is it possible to map these files using bwa mem on galaxy?

alignment • 44 views
ADD COMMENTlink modified 11 days ago by Devon Ryan1.9k • written 12 days ago by mychung0
1
gravatar for Devon Ryan
11 days ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Yes, bwa-mem can take a paired-end collection.

ADD COMMENTlink written 11 days ago by Devon Ryan1.9k

If read1 and read2 are in seperate fastq, then we specify each in the pair selection. For a fastq file contain both read1 and read2, how should the two reads be specified in the pair selection? Select the same fastq in both?

Thank you!

ADD REPLYlink written 11 days ago by mychung0

Select "paired interleaved" under "single or paired-end reads" will do.

ADD REPLYlink written 11 days ago by mychung0
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