Does ivar trim only from the ends of aligned BAM files?

[yl315504]

Hello,

The kit we are using will generate overlapped sequences. The reason is that the forward primers start at different location and the reverse primers have a fixed location. Please see an example below.

NC_045512.2 25 301 covid19genome_0-200_s0_M1 3 25 covid19genome_0-200_s0_M1F 301 322
NC_045512.2 56 301 covid19genome_0-200_s0_M2 33 56 covid19genome_0-200_s0_M2F 301 322
NC_045512.2 200 301 covid19genome_200-29703_s7490_U_88 182 200 covid19genome_200-29703_s7490_U_88F 301 322

If ivar also trims sequences in the middle, some sequences from (25, 301) will be trimmed because ivar will trim (182, 200), which is the primer sequence from the 3rd primer.

If ivar only trims from the ends (left and right), not the middle, we won't have any concerns.

Thanks,
Yan Liu
from UT Southwestern Medical Center, Dallas

[cmaceves]

Hi! So in the instance you're describing, if you have paired reads ivar will take the direction of the read into account. In other words for a reverse read, it will trim only the reverse primers (from the ends).

[xiaoziyayaya]

Hello，
ivar trim -b db/primers.bed -p sample.trimmed -i sample.sorted.bam，This command to produce the “sample.trimmed.sorted.bam ”file is not in strict accordance with the position of the primer to prune

The primer length is 18bp, but only 7bp was clipped,I noticed that the numerical description of XA was added to the resulting bam file, and I wonder if it is related to soft clipping？

Thanks,
ziman xing