Comments (2)
simoncchu
commented on July 30, 2024
It seems lots of Alu insertions reported from your results (vcf file having ~8000 records?). This is abnormal. We would expect to have around ~1200 germline Alu insertions for each sample. Those "errors" seems ok for me, as we don't expect Alu transductions, thus we didn't check the flanking regions.
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sidi-yang
commented on July 30, 2024
Sorry for the confusion. 8000 is the size of the file, about 8000 bytes. And about 20 somatic Alu insertion in the output. And thank you very much, I think the outputs are reasonable and correct:)) Thank you again!
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Related Issues (20)
- interpretation of GENE_INFO in output file HOT 1
- Long read cannot find temp files HOT 1
- xTea Long_read SyntaxWarning HOT 6
- line 1133, IOError: [Errno 2] No such file or directory: 'null' HOT 1
- x_TEA_main.py: error: no such option: --bamsnap HOT 2
- Very long length of L1 insertion HOT 1
- Long_reads: File detailing which reads show transductions of deletions HOT 1
- temp files burst out HOT 2
- Possible to merge TE sites and do genotyping in each sample? HOT 1
- xTea_long getting stuck, no errors, during wtpoa-cns, running HG38 HOT 2
- xTea output file understanding HOT 5
- About the case-control analysis in Illumina Short-read WGS Data HOT 3
- filtering HOT 4
- Will the coverage of BAM files affect the xTea results? HOT 3
- Input file for pseudogene insertion calling HOT 1
- Issue with Somatic Insertion Genotyping in Case-Control Mode HOT 3
- what's the meaning of "REF_REP=Fall_in_Alu_copy_2.5"? HOT 1
- Cannot find the target directory: xTea/xtea/genotyping/trained_model_ssc_py2_random_forest_two_category.pkl. HOT 3
- xTea for assembled genomes HOT 1
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