Question: Filter SAM or BAM
gravatar for hsuehyuanc
4.6 years ago by
United States
hsuehyuanc0 wrote:


I would like to know how to use the "Filter SAM or BAM" function

The only information I have is the MAPQ quality score = 255. I found only with the information, it is not enough to output the result file that I want or can be further processed.

Is there an introduction on how to use this function?

Thank you,



rna-seq galaxy filter • 2.4k views
ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by hsuehyuanc0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Change,

On the SAMTool -> Filter SAM tool form, click on the button "Add new flag". This will reset the form and a list of filtering options will be in the pull-down menu. You can filter on more than one flag at a time. If fact, this is common. 

For example, when performing variant analysis, a filter such as this might be used:


These are the same flag states described in the SAMTools documentation linked from the tool page, also found here (scroll down to SAM format):

Best, Jen, Galaxy team

ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson25k

Thank you Jennifer,

Actually my file is BAM. I think I need to do "Filter SAM or BAM" function before calculate the "inner distance between mate pairs" as the protocol shows to me.

How to do this?

What I have tried is to set the MAPQ score as 255 and then run. The output file is very small (106K) and i think it is nothing.

ADD REPLYlink written 4.6 years ago by hsuehyuanc0

MAPQ quality of 255 is useless information.

That field shows the mapping quality as a probablitity. The 255 is there because that version of software (bowtie1 most likely) is unable to fill it in correctly therefore puts the largest valid value there.

So forget about the MAPQ and move on to the next step.

ADD REPLYlink written 4.6 years ago by Istvan Albert250

Hi Jennifer, why did you selected "Read is paired" and "Read is mapped in proper pair". Would it be not enough only to use  the second?

ADD REPLYlink written 3.3 years ago by Mic70
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