GangSTR

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Hello, thanks for your time. I'm using GangSTR tool which is genome-wide profiling tandem repeats from short reads (Genotyping). I have couple of doubts: How can i know which loci...

kirannai

Issue about "Not enough reads extracted. Skipping locus.."

1

Hello GangSTR team, I am trying to apply GangSTR on **exome sequencing** samples. However, I encountered an issue about 'Not enough reads extracted' across all the TR regions. Could you...

tanlaboratory

Hi, I am trying to use GangSTR to identify a 52bp long STR in several samples. I have dentified my desired STR using the UCSC genome browser and repeatmasker (link:...

DomManou

Hi, I am attempting to use GangSTR-2.5.0 and ive encountered a strange issue where the REF and ALT alelles in the output VCF are being reported as numbers rather than...

alexpiper

According to this closed issue #107 it is an expected behaviour for GangSTR to fail with an error if the aligned reads in the input BAM file have not all...

dboceck

Are reads marked as duplicates filtered in GangSTR? It seems that such reads are not filtered. Thanks!

zhpn1024

Hi, i'm used to run gangstr on my bam files but recently we tried experiment by trimming our fastq sequences from 150bp to 100bp and 75bp and with these new...

CocoMlle

HELP

3

My experimental data is not whole genome sequencing but restriction site-associated DNA sequencing (RAD-seq), and I would like to know if I can use your software under such conditions. Thanks...

zhangjinpengGithub

str::out_of_range

2

For some samples I have this error. I don't know the reason and how to fix it. Here is the error message: terminate called after throwing an instance of 'std::out_of_range'...

mvcakir

Downstream filtering for haploid TRs

4

Nice tool! I Am trying to implement this tool for identifying TRs expansion in a bacterial genome. Though gangSTR works perfectly well, the problem is with subsequent filtering with dumpSTR...

Owuorgpo