Comments (6)
simoncchu
commented on July 30, 2024
I am not sure what's the depth of the file. If it is a sample of high depth, I would suggest trying with a larger memory.
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vaksmaz
commented on July 30, 2024
An increase in memory worked. It is using lots of ram, is that OK. Also, can you give a bit of information on the Long_Read output (example, what does this mean chr41584154715847572L1HS0R511~116 (see below) ). Most things are self evident but some are a bit hard to interpret. Which column is for gene annotation. etc...
Also, does long-read support somatic analysis?
6 66703922 LINE1 internal_inversion 4242:5324:+ 5328:6070:- CTATATCTTCTGGTAGAAACCTCAAGGCAAAATCAATTAGATTTCCAACT chr4~15841547~15847572~L1HS~0R~51~1~116 None TTTTTGGGGTAAGACCAATTTTTTATTTTCCCCGTCTTTGTCTAGGTTTCTACTATTCTATTTTCTCCATGGAACATATCTTTGAACAGCTTAGACTGGTCAGATATCTGCAAGATTGCTTTTTTTTTTTTTTTTTTCTTTGAGAGTTGTTTTTTATTTATTTTTTTTTTTTTTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCCCCCCCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCATCATTGTTGGACATTTGGGTTGGTTCCAAGCTTTGCTATTGTGAATAGTGCCGCAATAAACATACGTGTGCAGTGTCTTTATAGAAATGTTTATATCATTTGGGAAAAATTTCCCCAAAAGGGATGGCTGGGGCAAAAAGGGAAATTTTTAATTTAATCCCCGAGGAATCGCCACACTGACTTCCACAATGGTTGGAAATAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCCCATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGAACAAATTATGGGGGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAAGGAAATAAAAGAGGACACAAACAAATGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCCAAAGGAACAGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTACAAACCTGGAAAAAAAAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGTCATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATACTATATCTTCTGGTAGAAACCTCAAGGCAAAATCAATTAGATTTCCAACT GCAATCTTGCAGATATCTGACCAGTCTAAGCTGTTCAAAGATATGTTCCATGGAGAAAATAGAATAGTAGAAACCTAGACAAAGACGGGGAAAATAAAAAATTGGTCTTACCCCAA None clip_seq_with_polyA```
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simoncchu
commented on July 30, 2024
I have some notes here: https://github.com/parklab/xTea_paper/tree/main/run_tools/xTea/HG002 for the columns.
Long-read module doesn't have a somatic mode, which means it outputs combined germline and potential somatic. Also, it used a local assembly step, thus will miss the low VAF ones if the assembly step failed because of the low depth.
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vaksmaz
commented on July 30, 2024
And how do I interpret this chr4~15841547~15847572~L1HS~0R~51~1~116 in the example above?
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simoncchu
commented on July 30, 2024
It indicates this insertion contains a transduction region from a reference L1HS copy chr4:15841547-15847572, and the length of the transduction sequence is 116bp.
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vaksmaz
commented on July 30, 2024
Thank you very much for all the help.
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Related Issues (20)
- interpretation of GENE_INFO in output file HOT 1
- Long read cannot find temp files HOT 1
- 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
- Alu output didn't go through filter step? HOT 2
- 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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