Quality trimmer

[tahamasoodi]

Hi,

For trimming paired end sequences, isn't there chance of losing mate information? Say for example in a paired sequence, read 1 has a bad quality at the end while as read 2 is good. So, if we trim read 1, we may loose mate information since read 1 will be now shorter than read 2. Can anyone expalin it in detail?

Best,

[rajasereddy]

Hi

I can't understand the term mate information. Do you mean pairing information?

[tahamasoodi]

yes, I mean pairing information.

[GenoMax]

Some trimming programs may take out a read from a pair leaving an unbalanced number of reads in the corresponding files. That is why using a program (such as trimmomatic in paired-end mode) is important.

Uneven length reads are generally ok as long as both members of the pair are present.

[relipmoc]

Skewer is appropriate for your case

The information within paired-end reads may complement each other. So you don't need to do quality trimming before trimming adapters. In our unpublished evaluation, Skewer has the highest accuracy among all adapter trimmers for both single-end and paired-end reads. Furthermore, it is very fast when run in multiple thread mode.

Hi,

For trimming paired end sequences, isn't there chance of losing mate information? Say for example in a paired sequence, read 1 has a bad quality at the end while as read 2 is good. So, if we trim read 1, we may loose mate information since read 1 will be now shorter than read 2. Can anyone expalin it in detail?

Best,