[feature request] Further options to control trimming with consensus

[blex-max]

Would it be possible to implement a trim option to take a set number of bases after an initial trim threshold? e.g. for a sequence:

ACTGATCTACTAGATCCC

-q 5 -'crop' 10

we get:

~~ACTGA~~ TCTACTAGAT ~~CCC~~

Does that make sense? Thanks!

[tobiasrausch]

Can't you easily do this by simply using the length of the sequence to calculate the required right trimming size? E.g.:

tracy basecall -o out.fa -f fasta in.ab1 tail -n 1 out.fa | awk '{print length($1);}'

and then you do length - desired_left_trim - desired_length for the right trimming size?

[blex-max]

It seems convoluted (and computationally slow) to me to basecall the sequence, check the length, then use that length to feed into basecalling the same sequence again - but I suppose I could indeed do that!

[blex-max]

But to be clear I do still think it would be useful to have this be an internal feature

[ricardochinchillam]

Can't you easily do this by simply using the length of the sequence to calculate the required right trimming size? E.g.:

tracy basecall -o out.fa -f fasta in.ab1 tail -n 1 out.fa | awk '{print length($1);}'

and then you do length - desired_left_trim - desired_length for the right trimming size?

Can you give an example for this command? Because I'm interesting in trimming left and right of the sequence

[tobiasrausch]

For the consensus sub-command you can just specify the trimming length, i.e.:

tracy consensus --trimLeft1 50 --trimRight1 50 ...

Or do you want such an option for the FASTA output of tracy basecall ?