Comments (4)
bli25wisc
commented on September 12, 2024
Hi @jwisrael, can you use samtools view to extract the BAM record of "HWI:1:X:1:1216:4127:50166" and "HWI:1:X:1:1216:4180:50180" ?
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jwisrael
commented on September 12, 2024
Hi @bli25wisc here are the records:
HWI:1:X:1:1216:4127:50166 345 ENST00000262493.6 3092 255 77M268435404S * 0 0 AACTTAAAAAAAAAAGGAAAAAAGAAAAAAAAGCCCACGGGTCTTTGTAAG
DA>CDBDDFHJJJIHFGIJJJIHBIJJJJIHBHGHIJIGHHHHFDEFFCCC NH:i:1 HI:i:1
HWI:1:X:1:1216:4180:50180 419 ENST00000467733.1 268 0 50M = 326 109 GAAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAAGATGCTGTTT B@BDFFFFHHHFHHIJIGIIII?FFDHCHECHG3C>;DDCBG@@gd<?E? NH:i:6 HI:i:1
HWI:1:X:1:1216:4180:50180 339 ENST00000467733.1 326 0 51M = 268 -109 GTGACTCGAAAACTTTCTGAAGCTGATAATAGAAAGATGTCTCGGAAGGAG FFHIHIJIJJJIJJJJJJIIHGIEIIJJJIJJIJJJIGHHFHDDDDFFCCC NH:i:6 HI:i:1
HWI:1:X:1:1216:4180:50180 419 ENST00000496050.1 240 0 50M = 298 109 GAAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAAGATGCTGTTT B@BDFFFFHHHFHHIJIGIIII?FFDHCHECHG3C>;DDCBG@@gd<?E? NH:i:6 HI:i:2
HWI:1:X:1:1216:4180:50180 339 ENST00000496050.1 298 0 51M = 240 -109 GTGACTCGAAAACTTTCTGAAGCTGATAATAGAAAGATGTCTCGGAAGGAG FFHIHIJIJJJIJJJJJJIIHGIEIIJJJIJJIJJJIGHHFHDDDDFFCCC NH:i:6 HI:i:2
HWI:1:X:1:1216:4180:50180 419 ENST00000463503.1 216 0 50M = 274 109 GAAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAAGATGCTGTTT B@BDFFFFHHHFHHIJIGIIII?FFDHCHECHG3C>;DDCBG@@gd<?E? NH:i:6 HI:i:3
HWI:1:X:1:1216:4180:50180 339 ENST00000463503.1 274 0 51M = 216 -109 GTGACTCGAAAACTTTCTGAAGCTGATAATAGAAAGATGTCTCGGAAGGAG FFHIHIJIJJJIJJJJJJIIHGIEIIJJJIJJIJJJIGHHFHDDDDFFCCC NH:i:6 HI:i:3
HWI:1:X:1:1216:4180:50180 419 ENST00000476217.1 276 0 50M = 334 109 GAAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAAGATGCTGTTT B@BDFFFFHHHFHHIJIGIIII?FFDHCHECHG3C>;DDCBG@@gd<?E? NH:i:6 HI:i:4
HWI:1:X:1:1216:4180:50180 339 ENST00000476217.1 334 0 51M = 276 -109 GTGACTCGAAAACTTTCTGAAGCTGATAATAGAAAGATGTCTCGGAAGGAG FFHIHIJIJJJIJJJJJJIIHGIEIIJJJIJJIJJJIGHHFHDDDDFFCCC NH:i:6 HI:i:4
HWI:1:X:1:1216:4180:50180 419 ENST00000467789.1 300 0 50M = 358 109 GAAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAAGATGCTGTTT B@BDFFFFHHHFHHIJIGIIII?FFDHCHECHG3C>;DDCBG@@gd<?E? NH:i:6 HI:i:5
HWI:1:X:1:1216:4180:50180 339 ENST00000467789.1 358 0 51M = 300 -109 GTGACTCGAAAACTTTCTGAAGCTGATAATAGAAAGATGTCTCGGAAGGAG FFHIHIJIJJJIJJJJJJIIHGIEIIJJJIJJIJJJIGHHFHDDDDFFCCC NH:i:6 HI:i:5
HWI:1:X:1:1216:4180:50180 419 ENST00000265044.2 335 0 50M = 393 109 GAAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAAGATGCTGTTT B@BDFFFFHHHFHHIJIGIIII?FFDHCHECHG3C>;DDCBG@@gd<?E? NH:i:6 HI:i:6
HWI:1:X:1:1216:4180:50180 339 ENST00000265044.2 393 0 51M = 335 -109 GTGACTCGAAAACTTTCTGAAGCTGATAATAGAAAGATGTCTCGGAAGGAG FFHIHIJIJJJIJJJJJJIIHGIEIIJJJIJJIJJJIGHHFHDDDDFFCCC NH:i:6 HI:i:6
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bli25wisc
commented on September 12, 2024
Hi @jwisrael , I think this is a STAR aligner bug. The first alignment has CIGAR string "77M268435404S", which should not appear for transcript-based alignments. If you are not using the latest version of STAR, maybe you can consider update your program.
Hope it helps,
Bo
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jwisrael
commented on September 12, 2024
Hi @bli25wisc yes I think that fixed the problem. Thanks!
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