Questions about the tvr_consensus in tlens_by_allele.tsv file

[Flora076]

Hello Zach,
Wonderful software and I am using it for Schmidt’s data. I noticed that you have mentioned in other discussions to compare the FASTA file in the tel_reads.fa.gz file, with the supporting reads column from tlens_by_allele.tsv file, and pull the matched sequences out respectively.
I have a question regarding it, as there are more than 1ID in the supporting reads in the tsv file. I extracted the sequences but they are not the same, however they are still being clustered together. May I know why?
I got the following result from the tvr_consensus in the tsv file:

CCCCCCAAAAAAAAVVVVVVVVCCCCCCCGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCNNNNNNNNNNCCCNCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFCFFFFFFFFFFFFFFCFFFCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCVVVCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTTTTTTTTVVVVVVVCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCVVVVVVCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCVCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHVVVCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCLLLLLLLCCCCCCCCCCCCCCCCLLLLLLCCCCCCCCLLLCCCCCCCLLLLLLLLLLLLLLLLLLLCCCCMCLLLLLLLLLLLLLLLLLLLCCCLLLLLLLLLLLLCVVCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTTTTTTTTTTT

Canonical uses the Symbol C to represent the motif sequence TTAGGG. Does the C in the tsv_consensus reading above, represent the symbol or the C from the normal TCGA nitrogenous bases from DNA?
Are the colours in all_final_alleles.png, reflected in the extraction of the tsv_consensus?
I matched the tel_reads.fa.gz and ‘supporting reads’ column in tlens_by_allele.tsv, then reduced it by the sequence motifs into the respective symbols. However, my result is different from the sequence of tsv_consensus derived from the tsv file. Is there an explanation for the difference?

Looking forward to your clarification!
Thank you.
Flora

[zstephens]

Greetings! Would you be able to share the subset of reads belonging to this cluster? It's possible that reads from different alleles can wind up together depending on clustering parameters.

And indeed, the plots in all_final_alleles.png are using the tsv_consensus strings, and their associated colors from the source/resources/kmers.tsv file.

[Flora076]

This is the tsv file that was generated by Telogator2. tlens_by_allele-SRR26842330.tsv
I pulled out the first row data intel_reads.fa.gz, that were clustered together. first_row.tsv
How was the clustering done?

I am also trying to run the rest of Schmidt's data with the parameters -r ont -n 10 that were stated in the README. However, the time is still too long, even after I put the wall time as 168h. Is there perhaps a way to quicken the process and run time?

Thank you!