Add trimmed sequences to fastq header?

[js72587]

Is there a way to add the trimmed sequences (--clip_R1, --three_prime_clip_R1, etc.) to the fastq headers? It seems cutadapt has the --rename parameter to do this, but it doesn't look like TrimGalore has this option; is my understanding correct?

Thank you!

[FelixKrueger]

It doesn't have the this option right now, but it shouldn't be overly complicated to add (at least not for --clip_r1, --three_prime_clip_r1 and so on).

[js72587]

Thank you! That'd be great.

[FelixKrueger]

If I were to give this a go, what would you like to see? I could imagine something like:

if --clip_r1 or --clip_r2 is 1 or greater, we could add something like this to the header (here for --clip_r1 4:

:clip5:GATC

if --three_prime_clip_r1 or --three_prime_clip_r2 is 1 or greater, we could add something like this to the header (here for --three_prime_clip_r1 6:

:clip3:TAAATC

Or, if both 5' and 3' clipping were selected, add both like so:

:clip5:GATC:clip3:TAAATC

Does this sound useful?

[js72587]

Yes, that would be exactly what we're looking for. Thanks a lot!

[FelixKrueger]

Hi again. I have just added a new option --rename that should do exactly what outlined above. I have tried to make it work in single-end as well as paired-end mode (for use with --rrbs or --polyA). it should work for 5'-clipping (--clip_(r1/r2)) and 3'-clipping (--three_prime_clip_(r1/r2)), and combinations thereof. Furthermore, it should also work with --hardtrim5 and --hardtrim3, and hopefully help help with UMI handling.

Can you please clone the dev version, and let me know if it works in your hands?

[js72587]

Thanks so much for implementing this so quickly! I'll test it and will be back with feedback later this week. Really appreciated!

[js72587]

Hi Felix, I tested this and it works perfectly. Thank you so much!

[FelixKrueger]

Fantastic. It will find its way into the next release then. All the best!