Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Can we map fastq files with paired ends using bwa mem on galaxy?
0
gravatar for mychung
10 months ago by
mychung • 0
Taiwan
mychung • 0 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 • 523 views
ADD COMMENT • link •
modified 10 months ago by Devon Ryan • 1.9k • written 10 months ago by mychung • 0
1
gravatar for Devon Ryan
10 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

Yes, bwa-mem can take a paired-end collection.
ADD COMMENT • link written 10 months ago by Devon Ryan • 1.9k

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 REPLY • link written 10 months ago by mychung • 0

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

ADD REPLY • link written 10 months ago by mychung • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour