Question: Tool barcode splitter not recognizing inputs (PEAR-assembled reads)
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gravatar for michael.falta
2.1 years ago by
michael.falta10 wrote:

I ran an Illumina 2 x 250 PER on PCR amplicons and received the data demultiplexed by the Index on Read 2. The read 2 sequences were not quite long enough to reach the UMIs (barcodes) at the end of each sequence, so I then ran PEAR to assemble read 2 and read 1. The output clearly shows the additional nucleotides added to the end of read 2 with the barcodes present. However, when I use the Barcode Splitter tool on Galaxy, it does not even show the assembled file as a choice for “Library to Split.” Why is this not an option, ie., what have I done wrong? Is there an alternative way to achieve the result I am desiring?

I know that I can simply barcode split the reverse complement of the read 1 files, but it seems like I will be wasting the sequence information provided by read 2. Also, in a future experiment, I am going to have non-indexed sequence data. In that case, I will need the barcode information provided by read 1 plus the sequence information provided by read 2 (the amplicon is greater than the 2 x 150 PER we will be doing).

Thank you for your help. Michael

ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by michael.falta10
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The barcode splitter tool is expecting certain input datatypes. These are listed on the tool form. Double check the datatype metadata, assign the correct type, and the tool should pick up the inputs. How-to: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
1

Problem solved!!

Thank you, thank you, thank you....

The datatype for the assembled reads was fastq. I changed it to fastqsanger, and the barcode splitter worked perfectly.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by michael.falta10

Good news! Thanks for posting back what worked :) Jen

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
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