compare-tx-sites multiple replicates per condition

[marcellogiunta]

Hi,
thanks once ahain for introdicng compare-tx-sites! I have just starte playing with it to compare 2 conditions (3 bio rep per condition), with the following command

singularity exec -B ${BIND} ${DORADO_SIF} ${MODKIT} dmr compare-tx-sites
-a results/modkit_transcriptome/knockout_01.raw.bed.gz
-a results/modkit_transcriptome/knockout_02.raw.bed.gz
-a results/modkit_transcriptome/knockout_03.raw.bed.gz
-b results/modkit_transcriptome/ctrl_01.raw.bed.gz
-b results/modkit_transcriptome/ctrl_02.raw.bed.gz
-b results/modkit_transcriptome/ctrl_03.raw.bed.gz
--out ${OUTPUT_BED}
--gtf ${GTF}
--single-mod-code ${MOD_CODE}
--plot ${VOLCANO}
--log ${LOG}
--threads ${THREADS}

However I got this error message:
error: the argument '-a <COND_A>' cannot be used multiple times
Usage: modkit dmr compare-tx-sites [OPTIONS] -a <COND_A> -b <COND_B> --out <OUTPUT_TABLE> --gtf

Is it not possible to compare multiple replicates per condition? which syntax should I use for multiple replicates?

Thank you so much in advance!!

Best,
Marcello

[ArtRand]

Hello @marcellogiunta,

That's correct modkit dmr compare-tx-sites does not support replicates, yet. What I recommend is using modkit bedmethyl merge to combine the bedMethyls within a condition then use the pair of merged tables. If possible I'd use the build here since it has a bug fix to compare-tx-sites.

[marcellogiunta]

Hi @ArtRand ,
thanks, I ll try with the merging. Looking forward for a new version allowing to accept multiple replicates.
Thanks for you endless patienc and commitment.

Marcello

[marcellogiunta]

Hi @ArtRand,
two more questions.
Do you have an idea of when a version allowing to accept multiple replicates will be available?
In compare-tx-sites is not possible yet to specify a coverage threshold, right?

Thanks!

Marcello

[ArtRand]

Hello @marcellogiunta,

Do you have an idea of when a version allowing to accept multiple replicates will be available?

I can work on getting you a prototype.

In compare-tx-sites is not possible yet to specify a coverage threshold, right?

There is a flag for min valid coverage

[marcellogiunta]

Hi @ArtRand,
thank you so much, it would be amazing! I have also seen the update for the 0.6.4, very helpful!

Best,
Marcello