Closed HLHsieh closed 3 months ago
Sorry for the late reply. The FASTQ data is uploading to a cloud. When the progress is done, I’ll sent you the link. Best, Zilin Ren
On May 4, 2024, at 7:38 AM, HLHsieh @.***> wrote:
Hi there,
I am interested in this amazing tool. Could you please provide test data? Additionally, I'm curious if I can use this tool to determine the number of repeats on each allele.
Thank you, Hsin
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Hi there,
I'm really interested in this tool! I'd like to know if it's possible to use it to determine the number of repeats on each allele.
Additionally, I'm curious about how to obtain the repeat_structure.pat, panel_forenseq.csv, and threshold.cfg files. Could you please provide some guidance on obtaining these files and explain the meaning of each column in them, as well as in the output files like barcode01.txt and barcode01.log?
Regarding the output barcode01.txt from executing the sample code, it seems that for first several loci, no sequence is detected in the sample. Am I interpreting this correctly?
barcode,locus,seq,genotype,sn,sn_ratio barcode01,DYS19,<None>,<None>,0,<LowCov> barcode01,DYS390,<None>,<None>,0,<LowCov> barcode01,DYS391,<None>,<None>,0,<LowCov> barcode01,DYS392,<None>,<None>,1,<LowCov> barcode01,DYS437,<None>,<None>,0,<LowCov> barcode01,DYS438,<None>,<None>,0,<LowCov> barcode01,DYS439,<None>,<None>,0,<LowCov> barcode01,DYS448,<None>,<None>,2,<LowCov> barcode01,DYS460,<None>,<None>,0,<LowCov> barcode01,DYS481,<None>,<None>,0,<LowCov> barcode01,DYS505,<None>,<None>,0,<LowCov> barcode01,DYS522,<None>,<None>,0,<LowCov> barcode01,DYS533,<None>,<None>,0,<LowCov> barcode01,DYS549,<None>,<None>,0,<LowCov> barcode01,DYS570,<None>,<None>,0,<LowCov> barcode01,DXS8378,AAT [ATAG]9 TGA,9.0,870,1.0 barcode01,DXS8378,AAT [ATAG]11 TGA,11.0,570,0.65517 barcode01,DXS8378,AAT [ATAG]10 TGA,10.0,47,0.05402 barcode01,DXS8378,AAT [ATAG]8 TGA,8.0,24,0.02759 barcode01,HPRTB,TCT [ATCT]12 AAA,12.0,269,1.0 barcode01,HPRTB,TCT [ATCT]13 AAA,13.0,209,0.77695 barcode01,HPRTB,TCT [ATCT]11 AAA,11.0,28,0.10409 barcode01,HPRTB,TCT [ATCT]14 AAA,14.0,7,0.02602 barcode01,HPRTB,TCT [ATCT]10 AAA,10.0,6,0.0223
Thank you, Hsin
Hi Hsin, The files repeat_structure.pat and panel_forenseq.csv are organized manually, which can be found from the STRBase (https://strbase.nist.gov/). As for the cutoff file, we conducted a experiment for parameter inference, which is described in the manuscript. You can get access to the preprint version (https://www.biorxiv.org/content/10.1101/2023.11.04.565630v1) .
Log file outputs all genotyped alleles, while the txt file shows the final genotype of each locus. If the result shows
If you have any further questions, please contact me directly!
Best, Zilin
Hi there,
I'm really interested in this tool! I'd like to know if it's possible to use it to determine the number of repeats on each allele.
Additionally, I'm curious about how to obtain the repeat_structure.pat, panel_forenseq.csv, and threshold.cfg files. Could you please provide some guidance on obtaining these files and explain the meaning of each column in them, as well as in the output files like barcode01.txt and barcode01.log?
Regarding the output barcode01.txt from executing the sample code, it seems that for first several loci, no sequence is detected in the sample. Am I interpreting this correctly?
Thank you, Hsin