Trim Reads From BAM files

Question

[fusion.slope]

Hello,

am trying to trim the reads aligned to the genome from my bam files of different sizes (50 and 80 nucleotides). Am doing this with bamUtil:

./bam trimBam subset.bam subset.80.bp.from.Right.fwd.80.bp.from.left.rwd.bam -R 80

./bam trimBam subset.bam subset.80.bp.from.Right.fwd.80.bp.from.left.rwd.bam -R 50

the problem is that when i upload in IGV the new bam file with the sequences trimmed it has the same length of the not trimmed bam files. How is it possible to clearly see that the reads were trimmed?

In bamUtil tutorial it is written that the sequences will be trimmed and the nucleotide substitute with NNN (for all the 80 or 50 nucleotides). So basically what I need is to remove completely these 80 or 50 nucleotides in a way in which when i will visualize in IGV it is clear that the trimming happened.

Any idea is really appreciated?

[Brian Bushnell]

So, what exactly are you trying to do? And why?

[fusion.slope]

I am trying to remove noise from my peaks before performing the Peak calling. I have reads mapped in which I know that the information that i need is in the first ~20 nucletides (from the sequencing technique that we are using). So after mapping i want to remove all the other part of the reads (from the 21st nucleotide until the end of the read) that are not useful and might introduce noise in the peaks estimation.

[EagleEye]

Why don't you remove those sequence before mapping?? Is it ideal to remove the sequence after mapping and use it for peak calling (creating bias or manupulating the sample) !!