while converting transcripts.bam to genomic bam, rsem is throwing the following error and generating zero GB genome.bam file
A00804:42:HTMG2DSXX:4:1101:31584:1016's two mates are aligned to two different transcripts!
I tried to grep the reads that were actually aligning to different transcripts, they were RNA component of mitochondrial RNA processing endoribonuclease. How should I take care of them?
Error: "rsem-tbam2gbam /path/rsem /path/Contr_S14_L004.transcript.bam /path/last_rsem_test/Contr_S14_L004.genome.bam" failed! Plase check if you provide correct parameters/options for the pipeline!
where rsem is the name of my rsem human genome indices. Have replaced actual paths with '/path/'
while converting transcripts.bam to genomic bam, rsem is throwing the following error and generating zero GB genome.bam file
I tried to grep the reads that were actually aligning to different transcripts, they were RNA component of mitochondrial RNA processing endoribonuclease. How should I take care of them?
A00804:42:HTMG2DSXX:4:1101:31584:1016 83 ENST00000363046.1 124 12 120M = 124 -120 CCCGCTTCCCACTCCAAAGTCCGCCAAGAAGCGTATCCCGCTGAGCGGCGTGGCGCGGGGGCGTCATCCGTCAGCTCCCTCTAGTTACGCAGGCAGTGCGTGTCCGCGCACCAACCACNC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F NH:i:2 HI:i:1 ZW:f:0.934481 A00804:42:HTMG2DSXX:4:1101:31584:1016 163 ENST00000363046.1 124 12 120M = 124 120CCCGCTTCCCACTCCAAAGTCCGCCAAGAAGCGTATCCCGCTGAGCGGCGTGGCGCGGGGGCGTCATCCGTCAGCTCCCTCTAGTTACGCAGGCAGTGCGTGTCCGCGCACCAACCACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:2 HI:i:1 ZW:f:0.934481 A00804:42:HTMG2DSXX:4:1101:31584:1016 339 ENST00000602361.1 125 0 120M = 125 -120 CCCGCTTCCCACTCCAAAGTCCGCCAAGAAGCGTATCCCGCTGAGCGGCGTGGCGCGGGGGCGTCATCCGTCAGCTCCCTCTAGTTACGCAGGCAGTGCGTGTCCGCGCACCAACCACNC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#F NH:i:2 HI:i:2 ZW:f:0.0655191 A00804:42:HTMG2DSXX:4:1101:31584:1016 419 ENST00000602361.1 125 0 120M = 125 120CCCGCTTCCCACTCCAAAGTCCGCCAAGAAGCGTATCCCGCTGAGCGGCGTGGCGCGGGGGCGTCATCCGTCAGCTCCCTCTAGTTACGCAGGCAGTGCGTGTCCGCGCACCAACCACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:2 HI:i:2 ZW:f:0.0655191Error: "rsem-tbam2gbam /path/rsem /path/Contr_S14_L004.transcript.bam /path/last_rsem_test/Contr_S14_L004.genome.bam" failed! Plase check if you provide correct parameters/options for the pipeline!
where rsem is the name of my rsem human genome indices. Have replaced actual paths with '/path/'