est_library_size

[danteb...@gmail.com]

The est_library_size has two numbers separated by a hyphen.  The second of these numbers appears in the standard output as “Total TCR reads extracted”.  What is the first number?

[Bo Li]

The first number is the total number of reads used by TRUST to assemble TCR CDR3s. The second number is the total number of reads in the TCR locus. You may use either to calculate CPK, as long as you are consistent.

On Tue, Aug 15, 2017 at 5:49 PM, <danteb...@gmail.com> wrote:

The est_library_size has two numbers separated by a hyphen.  The second of these numbers appears in the standard output as “Total TCR reads extracted”.  What is the first number?

--
You received this message because you are subscribed to the Google Groups "TRUST for T cell receptor hypervariable region assembly" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trusttcr+unsubscribe@googlegroups.com.
To post to this group, send email to trus...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/trusttcr/dc3032b4-75fb-4375-91f2-cfb99ba29012%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[asaf...@gmail.com]

Hi Bo Li, 

Just to clarify regarding the CPK calculation - is it the unique TCR reads divided by the est_library_size? Do you multiply that number by a certain factor? In our dataset the calculation above results in CPKs of ~0.01 to 0.05, whereas I saw that you had values up to 10 in the first paper. I am wondering where the difference may be coming from. 

Thank you, 

Asaf

On Tuesday, August 15, 2017 at 6:06:09 PM UTC-4, Bo Li wrote:

The first number is the total number of reads used by TRUST to assemble TCR CDR3s. The second number is the total number of reads in the TCR locus. You may use either to calculate CPK, as long as you are consistent.

On Tue, Aug 15, 2017 at 5:49 PM, <danteb...@gmail.com> wrote:

The est_library_size has two numbers separated by a hyphen.  The second of these numbers appears in the standard output as “Total TCR reads extracted”.  What is the first number?

--
You received this message because you are subscribed to the Google Groups "TRUST for T cell receptor hypervariable region assembly" group.

To unsubscribe from this group and stop receiving emails from it, send an email to trusttcr+u...@googlegroups.com.

[Bo Li]

Hi Asaf,

You are right -- we multiply it by 1000, according to how CPK is defined. So you will get pretty similar range as what we have reported.

Thanks,

Bo

To unsubscribe from this group and stop receiving emails from it, send an email to trusttcr+unsubscribe@googlegroups.com.

To post to this group, send email to trus...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/trusttcr/cf285c14-09f9-41ca-9d8d-6f819bc24aee%40googlegroups.com.