Support for alternate chromosome names?

[skpeterson]

I am using GCF_009914755.1_T2T-CHM13v2.0 as my reference where the chromosme nomenclature is as follows

`
(base) [skpet@longleaf-login6 GCF_009914755.1]$ grep "^>" GCF_009914755.1_T2T-CHM13v2.0_genomic.fna | cut -d " " -f 1

NC_060925.1
NC_060926.1
NC_060927.1
NC_060928.1
NC_060929.1
NC_060930.1
NC_060931.1
NC_060932.1
NC_060933.1
NC_060934.1
NC_060935.1
NC_060936.1
NC_060937.1
NC_060938.1
NC_060939.1
NC_060940.1
NC_060941.1
NC_060942.1
NC_060943.1
NC_060944.1
NC_060945.1
NC_060946.1
NC_060947.1
NC_060948.1
`

does your tool support chromosme nomenclature other than chr1, chr2 etc

[skpeterson]

One more question about the tool usage. I have already identified motif repeat regions of the genome for my motif of interest based on the reference and compared these to TRF results based on the reference. I am however curious to see if there are any unidentified locations of my motif repeat in the genome based on long read sequencing of two cell lines.

My motif is a 4-mer and I am interested if there are unknown occurrance of 4 or more of the 4-mer throughout the genome not represented in the reference.

Can I run straglr using the following command

Run Straglr

python /nas/longleaf/home/skpet/software/straglr/straglr.py
"$BAM" "$FASTA" "$OUT_PREFIX"
--min_str_len 4
--max_str_len 4
--min_ins_size 16
--genotype_in_size
--min_support 2
--max_num_clusters 2
--nprocs 32

and then filter the output for my specific 4-mer motif of interest?

Hope that makes sense! Any thoughts are appreciated!

[readmanchiu]

if you're specifically looking for 4mer, setting both the min and max str length to 4 is correct.
By specifying min_ins_size 16 you are looking for motifs at least 4 copies more than the reference. Because long reads are usually noisy, a 16bp insertion is kind less reliable. I would suggest at least 50bp or even 100bp for --min_ins_size.
The other parameters look good.

[readmanchiu]

As for the question on chromosomes, please add --include_alt_chroms to your run, this should include chromosomes with underscores in their names in the analysis.