seqtk telo can't find results with my data

[ksc289]

Hi :)
I have used the following command:
seqtk telo assembly.fa > telo.bed 2 > telo.count

I instantly get two files: telo.bed (empty) and telo.count which shows me the following:
more telo.count
0 1272251157

Why can't you find telomeres in my assembly?

Thank you so much,
Karen.

[shenwei356]

seqtk telo assembly.fa > telo.bed 2 > telo.count

I think there should be no space between 2 and >.

Why can't you find telomeres in my assembly?

It could be in a more polite way, like "Why's no telomere repeat found?".

The reason might simply be no targets are detected in the current algorithm and parameters. I also tested with a T2T human chromosome, and it worked.

[arslan9732]

Try with other telomeric motifs. It is not necessary that the default motif (TTAGGG) is present in your assembly. You can try followings:
CCCTAAA
AAATCCC
TAGGC
....

[Sung-hub]

Could you tell me how to choose/switch telomeric motif sequence (I want to search) other than default motif?

[arslan9732]

@Sung-hub
seqtk telo -m CCCTAAA genome.fa

[Sung-hub]

Thank you for your response! I tried some possible telomeric sequence and I did not get any hit.
[sung.shin@arsnecla0ap2 200088meta_Tangled_contigs]$ seqtk telo -m CCCCAAT all_tangel_200088.fasta
0 374789249
[sung.shin@arsnecla0ap2 200088meta_Tangled_contigs]$ seqtk telo -m CCCAATC all_tangel_200088.fasta
0 374789249
[sung.shin@arsnecla0ap2 200088meta_Tangled_contigs]$ seqtk telo -m AAAT all_tangel_200088.fasta
0 374789249
[sung.shin@arsnecla0ap2 200088meta_Tangled_contigs]$ seqtk telo -m AAAATAAA all_tangel_200088.fasta
0 374789249
[sung.shin@arsnecla0ap2 200088meta_Tangled_contigs]$ seqtk telo -m TGGGGAT all_tangel_200088.fasta
0 374789249

I know those sequences are frequently in the assembly, but they might not be exactly at the end of contig (mostly several hundred bases inside). Does the location of telomeric sequence can be problem to identify with seqtk telo?

[arslan9732]

seqtk Only look at the end of the sequence. Manually look at your sequence's ends. Most probably you lost telomeric sequences during scaffolding (which usually happened).