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Old 09-01-2014, 06:17 AM   #1
super0925
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Location: UK

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Default Too many "no barcode" reads after running sequencing?

Hi All

I am analysing the RNA-Seq from Ion Proton.

The output file of each running is shown as follows (figure 1)Untitled.png


I think the RNA_Barcode_None_001 is the sample file I need to do analysis, am I right?

Question 1: But what is the other fastq file (barcode name: no barcode)?

And for this figure (figure 2),
Question 2: is this output file contain two samples?

However, if the '' No barcode '' file is very big (figure 3) , The QC plot of 'No barcode' and 'RNA_Barcode_None_001' are separately shown in figure 4 and figure 5.

Question 3: is it normal? What happened? Could it be wrong label or a bad sample or an unseccessful sequencing?


Thank you!
Attached Images
File Type: png fig1.png (22.0 KB, 13 views)
File Type: png figure2.png (27.9 KB, 7 views)
File Type: png fig3.png (23.5 KB, 6 views)
File Type: png per_base_quality1.png (10.9 KB, 5 views)
File Type: png per_base_quality.png (9.4 KB, 2 views)

Last edited by super0925; 09-01-2014 at 07:35 AM.
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Old 09-01-2014, 02:32 PM   #2
RemitoAmigo
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Hi super,

What seems normal for RNA is your figure2..where the IonXpress barcodes are listed.

You should have links at the bottom of the report for .bam files for each barcodes which you can convert to fastq files if you wish(I use Picard for that)...

Remito
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Old 09-02-2014, 02:24 AM   #3
super0925
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Quote:
Originally Posted by RemitoAmigo View Post
Hi super,

What seems normal for RNA is your figure2..where the IonXpress barcodes are listed.

You should have links at the bottom of the report for .bam files for each barcodes which you can convert to fastq files if you wish(I use Picard for that)...

Remito
I think when running barcoded RNA samples one needs to specify "IonXpress RNA" barcodes in the plan run; instead, if RNA libraries are notbarcoded, one should specify "RNA_Barcode_None".
Howver, in figure 3, i.e. my sample, I don't know is it useful to run analysis on the ‘no barcode’ reads (I thought it is the sample data), cause I think "Barcode_None" is not sample file
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