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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
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rsem-prepare-reference with a fasta transcript #87

Closed geparada closed 6 years ago

geparada commented 6 years ago

Hello deweylab!

I'm having an issue when I try to prepare a reference from a gene annotated transcripts in a fasta file. For instance here I just have one transcript as a test (named test.fa)

>ENSMUST00000072578.7 GCCAATCCCATCATCCCTGACCAACTGTCACCCTCCCGAGCTGCGCAAGCTGCGTCGGTCTGTGATACCGCTACTGGCACGAGCCCTGGGCAGAGGGTCCGGCGGAGGGATCCGCAGAGGCTAAGGTCTCAGAAGAAGAGTCAGCTACTGCGGCAGCACAAAAAAGGCGGCTACAGGGTGATGCGACAACCGATGTGAAGACAGATACAGTGCCCACGGTGGCTGGCCCGGAAGCTGAGTGGGCCTCGGCCCTCAGCGCATTCTGCCAGGGCCAGGCCAGAACTGCCTGCCTCCTCTTCTGCGGCTGATCCAAAACCAGCAAGGCAGCCCCAGGCCCTCGGTGCCTGCCTCCTTCCACCTGGGGCCTACCAAGACAGCCTTCCACCATGGCTCTGAAGAGAATCCACAAGGAACTGAACGACCTGGCCCAGGATCCCCCAGCACAGTGTTCAGCAGGTCCTGTCGGGGAAGATATGTTTCACTGGCAAGCTACAATCATGGGGCCAAATGATAGTCCCTATCAGGGCGGAGCATTTTTCTTGACAATTGATTTCCCAACAGAGTACCCCTTCAAACCACCTAAGGTTGAATTTACAACAAGAATTTATCATCCAAATGTTAACAGTAACGGCAGTATTTGTCTTGATATTCTTCGGTCACAGTGGTCTCCAGCACTAACTATTTCCAAAGTACTTTTGTCCATCAGTTCTCTGTTGTGTGACCCCAATCCAGATGATCCCTTAGTGCCTGAGATTGCTCAGATCTACAAAACAGATAGAGACAAGTACAACAGAACAGCTCGGGAATGGACTCAGAAATATGCGATGTGACTAAAGAGAATACTGGATATCCTCTACAAATAAAAGCTAGGGGAACTCTGAAAGAGAAGTTCTTTTGATTCCCACCGGACTGTTTCCCATGAACCCACGCCCACGCTGTACCTGCCTCATCCTCCCTGGTGCACCGTCTTCACCTGATACAGTACCGCTGCATGTTGCACGCACCAGAAATACTGTACCAACACTGTCTCCTAGCAGACGAGCGTTCTCCAGGCATAACCTGGATGTGAGATTAAAAGTTTTCCTTATTGACTTAAATCTGGATAACCACAAGGTGTGAGGGTGGTGGGTACACAATACTGCTCAGAAGGGGTAAAGGTCCCCCAATCTATAAGAGACAATGAGATTGCTTTTAAGTGGAAGCCATTTAAATTTAAATTTTTTTAATTTATA

But when I try to run rsem-prepare-reference test.fa test, I get this error:

rsem-synthesis-reference-transcripts test 0 0 test.fa Sequence ENSMUST00000072578.7 contains an unknown letter (ASCII code 13) at 0-based position 1677! "rsem-synthesis-reference-transcripts test 0 0 test.fa" failed! Plase check if you provide correct parameters/options for the pipeline!

Also other people is having the same error:

https://groups.google.com/forum/#!topic/rsem-users/sOjD9Kh8vrc

Are we doing something wrong?

Thanks for your help!

bli25wisc commented 6 years ago

@geparada, your file ends with '\r\n' instead of '\n'. It should work if you remove '\r'.