Question: Tophat mismatches for whole read vs segments
0
gravatar for Suzanne Gomes
4.2 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

Hi, I have been wondering this for a while, but can't seem to find an answer.

I wanted to map my reads in TopHat with a maximum of 2 mismatches in the entire (100bp) read. In galaxy, I set "Number of mismatches allowed in each segment alignment for reads mapped independently = 2" which seems to correspond to "--segment-mismatches". So does that mean that if segment length is se to default (25), then for my 100bp reads the maximum number of mismatches could be up to 8? This is how I ran my analysis, but after re-reading the Tophat documentation it seems like this might not be giving me what I want. Based on the documentation, it sounds like in order to get max 2 mismatches along the entire 100bp, it would be done by setting --read-mismatches to 2. But I see no option to set --read-mismatches in galaxy.

Is there a way for me to set '--read-mismatches' on galaxy? Or should I set my segment length to 100 and just leave "--segment-mismatches" set to 2? Or is it fine the way I did it, and I'm just misunderstanding something?

 

Thanks! 

rna-seq tophat • 1.9k views
ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by Suzanne Gomes120
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

On the Tophat tool form, open up the 'TopHat settings to use: Full parameters list" option. The form will reset. Near the top is the option "Final read mismatches:".

Hopefully this helps,

Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
0
gravatar for Suzanne Gomes
4.2 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

I just checked, and don't see that option on the older version of TopHat. It looks like it is only available on TopHat 2? I have been using the earlier version, but I will try again using TopHat 2. 

Thanks for your help! 

ADD COMMENTlink written 4.2 years ago by Suzanne Gomes120
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Correct, this is for Tophat2. The documentation you are looking at is probably also for Tophat2 - it can be confusing sometimes at the website.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
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