Details on -c

[000generic]

Hi!

I am using TPM Calculator for the first time on 83 bam files composed of over 475 NCBI SRR datasets from different researchers and Illumina technologies. Ideally, read lengths for these data sets are 200 bp but of course it varies in the specifics. I haven't yet checked them all or determined max-min ranges for them all - but have been seeing average read length values from STAR of 195 or 196 - but also a 181.

For TPM Calculator's -c option:

-c Smaller size allowed for an intron created for genes. Default: 16. We recommend to use the reads length

I'm wondering if I could get details on how the -c option impacts the TPM count process and how critical it is to optimize it for a given BAM file vs. simply running things default - or simple running a single value across all BAM files - say 150 to be generally under the read length of the vast majority of reads but much closer to a given actual read length than the default of 16.

I greatly appreciate any guidance or suggestions!

Thank you very much :) Eric