Entering edit mode
Hello,
I am running into some trouble using SGSeq::getBamInfo.
> getBamInfo(df) Warning message: Custom tag 'XS' not found in BAM file: '' Spliced alignments must include a custom tag 'XS'. Compatible BAM files can be obtained with an alignment program for RNA-seq data (e.g. GSNAP, HISAT, STAR, TopHat).
This is strange because I used STAR aligner and can see from samtools view output that the BAM files do in fact have the `Custom tag 'XS'` What could be the problem?
$ samtools view ~/scratch/NeoGeo/BAM/CD19/CD19_KTP-33_S14_L00.bam | head -10 NB501378:127:HL3WTAFXX:2:21104:15141:15869 163 chr16 28931963 255 75M = 28932344 445 CCTGCGCGAAGCTGGGTGCCCCGGAGAGTCTGACCACCATGCCCCCTACTCGCCACCACTTCTTCCTCCGCTTCC AAAAA6EEA/EAE6E6EEEEAEEEEEE/EEEA//E/AEE//EE/6EE/</E/<A/A//EEEAE<EA////EEA<E NH:i:1 HI:i:1 AS:i:123 NM:i:5 MD:Z:43A3C6T2T11T5 NB501378:127:HL3WTAFXX:3:11602:9797:7135 163 chr16 28931984 255 76M = 28932376 468 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE/EEEA NH:i:1 HI:i:1 AS:i:150 NM:i:0 MD:Z:76 NB501378:127:HL3WTAFXX:1:11107:12902:5751 163 chr16 28931984 255 76M = 28932376 468 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEEE6EEEEEEEEEE/<EEEEEEEEEEAEEEEEEEEAEEAEEEEAEE/E/EAEEAE<EA<EEA</A/EA NH:i:1 HI:i:1 AS:i:150 NM:i:0 MD:Z:76 NB501378:127:HL3WTAFXX:4:11410:13267:13851 163 chr16 28931984 255 76M = 28932075 424 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEEAAEEAAEAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE/EEEEEE/EEEEEA/AEEE/ NH:i:1 HI:i:1 AS:i:152 NM:i:0 MD:Z:76 XS:A:+ NB501378:127:HL3WTAFXX:2:11310:16325:17106 163 chr16 28931984 255 76M = 28932375 467 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEE//EAEEE6EEEE/EEEEEEEEEEAEAEEEEEAEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEAEEA NH:i:1 HI:i:1 AS:i:150 NM:i:0 MD:Z:76 NB501378:127:HL3WTAFXX:3:21412:2893:17606 163 chr16 28931984 255 76M = 28932075 424 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCACTACTTCCTCCTCTTCCTCACCCCCAAGGAAGACACGCC AA/AAEA/EEEEE/E/EEA/EEE<EEEEEEEA</EE////E6EAA<<//E/<EE/EEEAAEEA/<EEE//AE/EEE NH:i:1 HI:i:1 AS:i:140 NM:i:5 MD:Z:36T2T23T5T2G3 XS:A:+ NB501378:127:HL3WTAFXX:1:11306:16231:6320 163 chr16 28931984 255 76M = 28932350 442 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE/E/EEEEEEEEE/EE<E//AEE NH:i:1 HI:i:1 AS:i:150 NM:i:0 MD:Z:76 NB501378:127:HL3WTAFXX:4:11512:14545:4425 163 chr16 28931984 255 76M = 28932362 453 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEA/EEEEEAEEE/EEAE<EEEE NH:i:1 HI:i:1 AS:i:149 NM:i:0 MD:Z:76 NB501378:127:HL3WTAFXX:2:21304:13368:17224 163 chr16 28931984 255 76M = 28932362 453 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAA/EEEAAEEE/EE/EEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEE6EEEEE/EEEEAEEEAEE<E</EE NH:i:1 HI:i:1 AS:i:149 NM:i:0 MD:Z:76 NB501378:127:HL3WTAFXX:1:21106:16530:11344 163 chr16 28931984 255 76M = 28932350 442 CGGAGAGTCTGACCACCATGCCACCTCCTCGCCTCCTCTTCTTCCTCCTCTTCCTCACCCCCATGGAAGTCAGGCC AAAAAEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEE/AEEEAEEEEEEEE NH:i:1 HI:i:1 AS:i:148 NM:i:0 MD:Z:76