Question: Multiple fastq file for mapping with Bowtie2
gravatar for mgmehta
3.1 years ago by
United States
mgmehta0 wrote:



I have some amplicon sequences for 144 samples that I would like to map on to a reference gene to identify SNPs. For this I am planning on using Bowtie2 in galaxy for the mapping part and then use  Sams tools- mpileup for the snp calling. My question is that i am currently struggling to map multiple fastq files simultaneously with Bowtie2, it only lets me done one at a time. Can I map multiple input fastq file with Bowtie2 in galaxy instance?


Thank in advance for the help!


bowtie • 1.8k views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by mgmehta0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You can use multiple file inputs or dataset collections. Please see the details for how-to in the Galax wiki here:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k

HI, just a followup on the above question.

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 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. Is the similar possible in galaxy?

THanks! Bala

ADD REPLYlink written 2.3 years ago by balaszone60
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