JOSS-Statement of need

[sridhar0605]

[Statement of need]
I see that the original methylseq has a baked in qualimap QC tool, could you please explain what additional QC is target-methylseq-qc offering that is going to helpful.

[abhi18av]

Hi @sridhar0605 , thank you for this question.

I've just come back from a break and still catching up; please allow me some time to circle back on this question after discussing with co-authors.

CC @agudeloromero

[abhi18av]

Hi @sridhar0605

Apologies for the late response here, but happy to respond back with our answer after some internal discussions.

I see that the original methylseq has a baked in qualimap QC tool,

Indeed, this is correct. The point we wish to highlight is that methylseq pipeline includes the alignment step and therefore the Qualimap QC is used for evaluating the quality of generated BAM files.

However, in the case of the target-methylseq-qc pipeline, (i) the picard_profiler mode uses the pre-existing BAM files to calculate the coverage with respect to an existing reference FASTA (ii) and the bed_filter mode relies directly on the raw BED file to generate the BED file for for the provided sequencing panel which in our study was Human TWIST methylseq panel.

Therefore, with the target-methylseq-qc pipeline, we aimed to diversify the post-processing steps after the initial methylseq pipeline for targeted sequencing.

[sridhar0605]

Thanks @abhi18av et al closing. Great work!