Error with Filter tool from galaxy

Question: Error with Filter tool from galaxy

3.4 years ago by

marcioslash • 0

marcioslash • 0 wrote:

I new user in galaxy, so a i'm having a problem with it

I'm analysing NGS Data, so:

1 - I uploaded the files into my galaxy account

2 - Use Fastqc to verify quality

3 - Filtered the reads using Filter FASTQ - minimum score 30 - and cut 9 nt from 5' end

4 - Use Fastqc again to verify quality

Everything is ok ... the box plot from my reads are all ok in galaxy (all above 30) ...

But when i download my filtered file, the reads are all bellow 30, i'm getting only the bad ones, the good ones, stay in galaxy, there is no option to get the right file, it just download the wrong one

Some one could help me with this problem ??

fastq fastqc qa filter galaxy • 1.0k views

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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by marcioslash • 0

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This seems very odd. Would you please share a history with galaxy-bugs@list.galaxyproject.org? This is the Main Galaxy (http://usegalaxy.org) support list for sharing data on that server privately. Please include the link to this Biostars post and more details about which exact datasets you are downloading and describe how you are doing this in the user interface.

Thanks and hopefully we can help, Jen, Galaxy team

ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

3.4 years ago by

marcioslash • 0

marcioslash • 0 wrote:

Here is the history

https://usegalaxy.org/u/marcio-godinho/h/ngsvirus

ADD COMMENT • link written 3.4 years ago by marcioslash • 0

Which file are you downloading that is not a match for what is in Galaxy? Thanks, Jen

ADD REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

70: Filter FASTQ on data 25

71: Filter FASTQ on data 29

When i download it to my computer and Run Fastqc, all reads bases are all below 18 quality !

ADD REPLY • link written 3.3 years ago by marcioslash • 0

For you, the file downloaded is actually different from what is on the Galaxy server for each dataset? I am unable to reproduce that.

Perhaps the settings for FastQC differ from those used in Galaxy? Click on the "i" info button for those runs to see the command line options used and compare to those that you use.

Jen

ADD REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Yes ... the reads filtered in this archive are all bellow 18, different from the reads that are in galaxy.

I tested it with Fastqc (same paramenters as galaxy) and i opened this file in Geneious ... the result is that all the bases are bad quality ...

I really dont know how i can downlad that reads that are good quality filtered

ADD REPLY • link written 3.3 years ago by marcioslash • 0

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