Extracting readnames from pindel

[robinweide]

Hi everybody, very short question:

Is there a possibility to get the 'mapped' readnames from pindel?
In that way, one could extract those reads from the unmapped-read pool.

[KaiYe]

Hi everybody, very short question:

Is there a possibility to get the 'mapped' readnames from pindel?
In that way, one could extract those reads from the unmapped-read pool.

in the Pindel raw output, read names are displayed for each read with split-read alignment. the string start with @ is read name.

let me know if you have any questions.

Kai

[robinweide]

Ah okay, didn't scrolled all the way to the right of your example output.

Another question: the CloseEndMapped- file... Are those the (former unmapped) reads, that are now split-mapped? And what about the RP-file?