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gymrek-lab/LongTR
Chromosome Nomenclature

Hello! I am using the T2T genome as my reference (GCF_009914755.1). The chromosome nomenclature in the NCBI T2T reference is refseq (NC_XX) and not UCSC (chrXX). When I try and run longSTR on my bam files ...
  • skpeterson
  • 1
  • Opened 
    5 days ago
  • #29

gymrek-lab/LongTR
How to ignore read groups

Hi, let s say my bam file contains 2 unique read group IDs for 2 unique libraries and 2 unique samples as for example a top off sequencing was necessary. Now I would like to genotype all reads in this ...
  • DennyPopp
  • 5
  • Opened 
    23 days ago
  • #28

gymrek-lab/LongTR
Visualization of LongTR genotypes

Is there a way to generate read visualizations for LongTR calls? I see VizAln and VizAlnPdf scripts in the repo, but don t see the --viz-out option that existed in HipSTR.
enhancement
  • bw2
  • 1
  • Opened 
    on Feb 19
  • #27

gymrek-lab/LongTR
Compilation issues

Hi, Thank you for developing this tool! I’m currently experiencing some challenges with compiling LongTR (Ubuntu 24.04.1). As I am relatively new to bioinformatics, I’m finding it a bit difficult to ...
  • leenput
  • 2
  • Opened 
    on Jan 27
  • #23

gymrek-lab/LongTR
repeat catalogs for T2T reference

Hi, Thank you for the nice tool! I am wondering if you have a repeat catalog bed file for T2T2 reference. LongTR requires motif length and motif count, which are not available in the current repeat catalog ...
  • ywzhang071394
  • 4
  • Opened 
    on Jan 22
  • #22

gymrek-lab/LongTR
Request optimized default alignment parameters for ONT data

The default settings for --alignment-params are optimized for PacBio HiFi reads. You suggest increasing the gap-open values f and g for ONT reads with a higher indel error rate, but it s not clear what ...
  • seboyden
  • 1
  • Opened 
    on Dec 18, 2024
  • #21

gymrek-lab/LongTR
Capability with Mixed Patterns

Hi there, I am curious if you have evaluated the performance on TR regions containing mixed patterns. Specifically, I am interested in its capability when dealing with regions that have simpler mixed ...
  • HLHsieh
  • 1
  • Opened 
    on Oct 27, 2024
  • #20

gymrek-lab/LongTR
LongTR v1.1 segfaults after "Processing flanking sequences"

Hello, When I run the latest LongTR v1.1, I get an exit code 11 (segfault) almost immediately after calling begins, right after Processing flanking sequences: ... Processing region chr1 16710 16743 29 ...
  • davidlougheed
  • 2
  • Opened 
    on Sep 25, 2024
  • #19

gymrek-lab/LongTR
Cannot git clone and build longTR

Cloning into spoa ... Warning: Permanently added the ECDSA host key for IP address 140.82.114.4 to the list of known hosts. git@github.com: Permission denied (publickey). fatal: Could not read from remote ...
  • Owuorgpo
  • 1
  • Opened 
    on Sep 25, 2024
  • #18

gymrek-lab/LongTR
Segmentation Fault when Running LongTR

I m encountering a segmentation fault when running LongTR with phased BAM tags to genotype and phase TRs. Below are the details of the command used and the error message. DIR=test_data ./LongTR --bams ...
  • almreis
  • 1
  • Opened 
    on Jul 10, 2024
  • #17
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