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Question: Need help with 'barcode splitter'
0
gravatar for phoenix
2.9 years ago by
phoenix • 0
phoenix • 0 wrote:

I have a Fastq dataset obtained from Miseq with 24 million reads. When I use the barcode splitter tool to split them to 3 groups, I found that the matched reads are only about 50k, 9k and 900 reads. There are 99% reads are unmatched.

But I manually check the first megabyte (about 4500 sequences), each of three barcode gets more than 1000 matched reads.

I have no idea with this problem. Any suggestion is welcome.

Feng
galaxy • 821 views
ADD COMMENT • link •
modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by phoenix • 0
0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello Feng,

This is odd and much could be the root cause for these results. We'd like to take a look. Is it reproducible at http://usegalaxy.org? Please try and if so, generate a shared history link and send that along with a link to this post plus some comments that note which datasets represent the odd output (be sure all inputs/outputs are left in an active state - none deleted/perm deleted) to galaxy-bugs@lists.galaxyproject.org and we can help troubleshoot.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hello, Jen,

I send an email with my Galaxy history to the email address you provided. The problem is still when I try to re-analyze the data.

Thank you for your help,

 

Feng

ADD REPLY • link written 2.8 years ago by phoenix • 0

Thanks Feng, I replied via email to the shared bug report from 2/5. 

The issue was the result of the first, but the second could present a problem. In the test history I shared back, both were corrected and that is how I suggest you also proceed.

1. The two columns of the input barcode dataset were separated by a space instead of a tab. This is always a problem.

2. The sequence of the barcodes included both upper and lower case bases. I converted all bases to be upper case. Conservative/strict formatting that follows the examples/descriptions in the help section of tools can never harm and helps to avoid issues in general.

Take care, Jen, Galaxy team

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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