Question: Cannot join combined R1 and R2 files
0
gravatar for casey.wright
4.4 years ago by
Australia
casey.wright0 wrote:

Hi Everyone,

 

From reading around, I'm not sure whether a solution has been found to the problem of the FASTq joiner tool.

I am trying to combine left and right reads from RNA-seq data into one file, before cutting my adapter sequences and aligning with Tophat.

 

As I had data across two lanes for 1 sample, i first concatenated files from both lanes for left and right reads respectively. I have then tried to join the concatenated datasets. My data is in the newer format.

Can anybody offer a solution to this problem?


Thank you for your help.

rna-seq • 1.5k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by casey.wright0
0
gravatar for Wolfgang Maier
4.4 years ago by
Germany
Wolfgang Maier600 wrote:

> As I had data across two lanes for 1 sample, i first concatenated files from both lanes for left and right reads respectively. I have then tried to join the concatenated datasets.

 

.. and what happened next ?

Provide an error message, then maybe someone can diagnose the problem.

ADD COMMENTlink written 4.4 years ago by Wolfgang Maier600
0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

You concatenated multiple right read datasets into one dataset, did the same for the left into a second dataset, and now the tool is not recognizing the input? The "datatype" needs to be in ".fastqsanger" for each. Confirm the quality scaling and either run the groomer or simply assign datatype. Instructions are here:

https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA 

Best, Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k
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