Hi Galaxy,

Ive got 2 problems for you;

1) Ive got microRNA Illumina NGS data that I want to analyse, I put it through 
fastQC on galaxy and it showed that 71% of the reads in one overrepresented 

         Percentage              Possible Source
71.06413061961005       RNA PCR Primer, Index 1 (100% over 29bp)
2.2106372475809497      RNA PCR Primer, Index 12 (100% over 44bp)
1.7497930632000402      RNA PCR Primer, Index 2 (100% over 34bp) 

What would be the best way to remove this contamination? Also is is still ok to 
use that data despite such high contamination? Ive currently been trying to 
remove the sequence by using the clip adaptor tool, using the following options;

library to clip 2: FASTQ Groomer on data H1
Minimum sequence length (after clipping, sequences shorter than this length 
will be discarded)  15
Enter custom clipping sequence  
enter non-zero value to keep the adapter sequence and x bases that follow it    0
Discard sequences with unknown (N) bases        No
Output options  Output only non-clipped sequences (i.e. sequences which did not 
contained the adapter)

Clipped reads - discarded.
Input: 23776583 reads.
Output: 3091831 reads.
discarded 1287140 too-short reads.
discarded 18984774 adapter-only reads.
discarded 412838 clipp

but then I'm only left with 13% of the reads.

2) After I've filtered and clipped the adapter I want to analyse the frequency 
of each miR. I've been using miranalyzer to do this, I use the following 

data=>groomer=>clip adapter=>filter FastQ (min quality 20)=>fastq to 

the collapse file is like this;


Then upload the collapse file to miranalyzer however the total reads in the 
miranalyzer output is the same as the total number of sequences in the collapse 
file, it doesn't seem to recognise the count number. 

miranalyzer says the following;
        2.1 Input formats
        miRanalyzer requires a single file containing the unique reads and 
their counts. The application accepts two different input formats:

        2.1.1 A tab or space separated file as in the following example 
(read-count format):

        GAGGTAGTAGGTTGTA        49862
        ACCCGTAGAACCGACC        15490
        ...     ...
        GGAGCATCTCTCGGTC        13762
        2.1.2 A multifasta file:

        >ID1    49862
        >ID2    15490
        >ID     13762
        The description field must hold the read count. If not set, it is 
supposed to be 1. The file must have extension ’fa’, ’fasta’ or ’mfa’.

Do you know how I could change my format so it can recognise the read count 
e.g. maybe change the '-' to a space?

3) Ive recently got the local install of galaxy but encounter the following 
error when I try to add a file to my data libary

Error attempting to display contents of library (New data library): 
(OperationalError) no such column: True u'SELECT dataset_permissions.id AS 
dataset_permissions_id, dataset_permissions.create_time AS 
dataset_permissions_create_time, dataset_permissions.update_time AS 
dataset_permissions_update_time, dataset_permissions.action AS 
dataset_permissions_action, dataset_permissions.dataset_id AS 
dataset_permissions_dataset_id, dataset_permissions.role_id AS 
dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND 
dataset_permissions.action = ?' ['access'].

Ive got the latest version of galaxy and am using chrome and mountain lion os x

changeset:   7986:12fcd068b12e
tag:         tip
user:        Daniel Blankenberg <d...@bx.psu.edu>
date:        Thu Oct 18 11:22:12 2012 -0400
summary:     Do not hide failed datasets with HideDatasetAction post job action.

Any help will be greatly appreciated

Thank you 
Rosie Griffiths

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