Paired-end dataset collection with Bowtie2

Question: Paired-end dataset collection with Bowtie2

3.1 years ago by

United States

Hi,

I made a paired-end fastqsanger dataset collection and tried to run it with Bowtie2, but it doesn't recognize the input files. Is that functionality of the tool really working or is it still in testing? I have also tried to use it with BWA and tophat and never got anything. I am wondering how it assigns the forward and reverse when the input is a list. I could not see how it assigns them in the wrapper.

Best,

Brigida Rusconi

bowtie collection • 1.1k views

ADD COMMENT • link •

modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by brigida.rusconi • 40

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

My guess is that the data is in a collection, but not a paired-end collection (the 3rd type). When building the paired list, orientation of the pairs is specified, and then that is interpreted by tools downstream.

Double check these two things:

1. The dataset collection was created with the option "Build list of dataset pairs". This creates a paired-end collection.

2. The target tool form has the input type selected as "Paired-End Dataset Collection".

Best, Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi,

I have done both as described above. It starts the Bowtie2, but when I look at the information and it says no dataset collection.

1. paired dataset collection link: https://www.dropbox.com/s/ovt3rzc69hesmns/Screenshot%202015-10-14%2012.49.58.png?dl=0

2. Bowtie2 settings link: https://www.dropbox.com/s/57ac3v6hmke9udf/Screenshot%202015-10-14%2012.50.39.png?dl=0

3. Bowtie2 info link: https://www.dropbox.com/s/chmjk7s1wy828o0/Screenshot%202015-10-14%2012.51.42.png?dl=0

The admin checked and it looks like Bowtie2 isn't starting it just stays in the currently running status, without actually running. I am not using fastqgroomer to prepare my files since they already have the sanger quality scores. I simply change the extension to fastqsanger.

ADD REPLY • link written 3.1 years ago by brigida.rusconi • 40

I tried again and it looks like I was not waiting long enough for it to finish. I was thrown off by the info saying no dataset collection. Thanks for the help.

ADD REPLY • link written 3.1 years ago by brigida.rusconi • 40

Ok, this makes sense if the info page screenshot was from when the job was still queued/executing. I thought the problem was with the tool form entry itself (before submission, meaning recognizing datasets from the history to be selected). But glad all is working! Jen

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »