Question: End Position of an alignment in BWA
0
gravatar for zampe_pfloyd
3.9 years ago by
zampe_pfloyd10
Canada
zampe_pfloyd10 wrote:

Hi,

Does someone know if there is a way in galaxy to add a column in a dataset (for example a BWA output) that indicates the end position for each alignment ?

Alternatively, I thought I could get around that problem by measuring the length of each alignment (calculate the number of bases in the sequence column and adding it to the start position). However the character count tool in text manipulation only calculates the number of characters for the whole dataset (not a specified column on each line...).

 

Does someone has an idea ??

 

Thank you!

bwa • 747 views
ADD COMMENTlink modified 3.9 years ago by Bjoern Gruening5.0k • written 3.9 years ago by zampe_pfloyd10
1
gravatar for Bjoern Gruening
3.9 years ago by
Bjoern Gruening5.0k
Germany
Bjoern Gruening5.0k wrote:

Hi,

which format do you want to obtain in the end. There should be a tool called 'BAM to BED' that will give you the start and end position of every alignment.

Cheers,

Bjoern
 

ADD COMMENTlink written 3.9 years ago by Bjoern Gruening5.0k
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