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alexdobin / STAR

RNA-seq aligner
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Why is there no assigned gene when the sequence can be completely aligned #2122

Open pandh0607 opened 2 months ago

pandh0607 commented 2 months ago

Hi Alex, Here's an example of one read with such a result. R1: @A00199:1025:HCCFMDSXC:4:1233:8956:32597 1:N:0:TCGCCTTA+CTAGCGCT ACAGCAGAAGGCCAGAGCATTCGATCCACGTGCTTGAGCACTTCGATTTGTGGGACAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGCCTCGGTGGGGCCCAGTTATAAGAAAAGCGGTGAGGACCAAATACAAAAAGGAAAT + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:,,F,,,,,,FF,:,:,F::,,,F,:F,F,:::,,,,::,,,,,,,:,FFF,,,,F,,

R2: @A00199:1025:HCCFMDSXC:4:1233:8956:32597 2:N:0:TCGCCTTA+CTAGCGCT TTTTGGAAGTGGTCCAGACCGCTGTTCTGATAACTGTGGCCCTCCGAGGG + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

ref fasta:

chr1003 1003 TTTTGGAAGTGGTCCAGACCGCTGTTCTGATAACTGTGGCCCTCCGAGGG

gtf: chr1003 HAVANA exon 1 50 . + . gene_id "ENSG00000101199"; transcript_id "c77eb74"; gene_name "ARFGAP1"

bam: A00199:1025:HCCFMDSXC:4:1233:8956:32597 0 chr1003 1 255 50M * 0 0 TTTTGGAAGTGGTCCAGACCGCTGTTCTGATAACTGTGGCCCTCCGAGGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF GX:Z:- GN:Z:- CB:Z:ACAGCAGA_CACTTCGA UB:Z:TTTGTGGGACAG

Thanks! pdh