R1 and R2 specific left and right trim values

[will-NYGC]

Is there a way to apply different (left|right)_trim values to R1 and R2?

[heathsc]

Not at the moment although this could be added without too much difficulty. For my curiosity, could you give a brief description of a situation where this would be useful?

Cheers, Simon

On Fri, Oct 2, 2020 at 1:10 PM will-NYGC notifications@github.com wrote:

Is there a way to apply different (left|right)_trim values to R1 and R2?

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[will-NYGC]

We are using the Swift Accel-NGS MethylSeq kit on cfDNA (short frags) which appends a synthetic oligo to the 3' end of ssDNA in order to ligate adapters (https://swiftbiosci.com/wp-content/uploads/2019/02/16-0853-Tail-Trim-Final-442019.pdf). This synthetic oligo appears at the end of R1 and beginnig of R2. Rather than hardclipping the reads, we thought we could avoid defects in methylation calling caused by this by using gemBS trim values. Currently we use bwameth+MethylDackel where this is possible but we like your full gemBS pipeline and would like to switch over.

[heathsc]

OK, let me think about the best way to implement this.

Simon

On Tue, Oct 6, 2020 at 4:13 PM will-NYGC notifications@github.com wrote:

We are using the Swift Accel-NGS MethylSeq kit on cfDNA (short frags) which appends a synthetic oligo to the 3' end of ssDNA in order to ligate adapters ( https://swiftbiosci.com/wp-content/uploads/2019/02/16-0853-Tail-Trim-Final-442019.pdf). This synthetic oligo appears at the end of R1 and beginnig of R2. Rather than hardclipping the reads, we thought we could avoid defects in methylation calling caused by this by using gemBS trim values. Currently we use bwameth+MethylDackel where this is possible but we like your full gemBS pipeline and would like to switch over.

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[heathsc]

This has now been added in 3.5.3. From gemBS or bs_call, left_trim and right_trim options can now take either 1 or 2 values. If 2 values are specified then this give the trim values for read 1 and read 2 respectively. If only 1 value is specified then both reads are trimmed using the same value for the trim parameter (i.e., the previous behaviour)