Question: Multiple fastq files in Bowtie2
gravatar for balaszone
2.3 years ago by
balaszone60 wrote:

I have 4 lanes in each set of reads. I do understand using the multiple datasets option will run all pairs, but each pair separately.

BUt what I want to achieve is little different -

There is a command line option in bowtie2 where if you give all lanes of R1 as one set of inputs(using option -1) and and all lanes of R2 as another set(using option -2) it will automatically process and provide only one *.bam file as output. Is the similar possible in galaxy?

Thanks! Bala

bowtie galaxy bam • 1.2k views
ADD COMMENTlink modified 2.3 years ago by Martin Čech ♦♦ 4.9k • written 2.3 years ago by balaszone60
gravatar for bryantl
2.3 years ago by
United States
bryantl90 wrote:

You could concatenate the datasets so that you are inputing one fastq file for R1 and one file for R2.

ADD COMMENTlink written 2.3 years ago by bryantl90

Yeah, I was aware of the concatenate process. But bowtie2 when run in command line has an option to take multiple inputs. I would want to know if the same is possible in galaxy. any help?

Tx Bala

ADD REPLYlink written 2.3 years ago by balaszone60
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