Hi,
I'm using miRDeep2 to find new miRs in Mouse genome. I have RNA seq data from Illumina.
I used mapper.pl to generate .fa and .arf files. Now I'm using miRDeep2.pl to find new miR's. But it shows that the arf format is incorrect.
Here are the commands I have used:
I get this error when I ran miRDeep2.pl:
This is the arf file of the sample:
I'm not sure what the error is. The arf file looks alright to me.
Does anyone know what the issue is? Any help appreciated. Thanks!
I'm using miRDeep2 to find new miRs in Mouse genome. I have RNA seq data from Illumina.
I used mapper.pl to generate .fa and .arf files. Now I'm using miRDeep2.pl to find new miR's. But it shows that the arf format is incorrect.
Here are the commands I have used:
Code:
mapper.pl SampleC.fastq -e -h -p ~/refs/mm9 -s SC.fa -t SC.arf
Code:
miRDeep2.pl Sample.fa ~/refs/mm9.fa Sample.arf miRBase_mmu_v20.fa none none -t Mouse
#####################################
# #
# miRDeep2.0.0.5 #
# #
# last change: 25/06/2012 #
# #
#####################################
miRDeep2 started at 13:57:10
#Starting miRDeep2
#Starting miRDeep2
/opt/sam/miRDeep/2.0.5/miRDeep2.pl SampleD.fa
/home/abc/refs/mm9.fa SampleD.arf ../miRBase_mmu_v20.fa none none -t Mouse
miRDeep2 started at 13:57:10
mkdir mirdeep_runs/run_07_05_2014_t_13_57_10
Error: Mapping file SampleD.arf is not in arf format
Each line of the mapping file must consist of the following fields
readID_wo_whitespaces length start end read_sequence genomicID_wo_whitspaces length start end genomic_sequence strand #mismatches editstring
The editstring is optional and must not be contained
The readID must end with _xNumber and is not allowed to contain whitespaces.
The genomeID is not allowed to contain whitespaces.
# #
# miRDeep2.0.0.5 #
# #
# last change: 25/06/2012 #
# #
#####################################
miRDeep2 started at 13:57:10
#Starting miRDeep2
#Starting miRDeep2
/opt/sam/miRDeep/2.0.5/miRDeep2.pl SampleD.fa
/home/abc/refs/mm9.fa SampleD.arf ../miRBase_mmu_v20.fa none none -t Mouse
miRDeep2 started at 13:57:10
mkdir mirdeep_runs/run_07_05_2014_t_13_57_10
Error: Mapping file SampleD.arf is not in arf format
Each line of the mapping file must consist of the following fields
readID_wo_whitespaces length start end read_sequence genomicID_wo_whitspaces length start end genomic_sequence strand #mismatches editstring
The editstring is optional and must not be contained
The readID must end with _xNumber and is not allowed to contain whitespaces.
The genomeID is not allowed to contain whitespaces.
This is the arf file of the sample:
[abc mirdeep2]$ head Sample.arf
seq_2 51 1 51 ggcaagggaagaagacttcaggccactgggaaatgcttggttctgttcagt chr4 51 133526049 133526099 ggcaagggaagaagacttcaggccactgggaaatgcttggttctgttcagt + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_5 51 1 51 gccattcttgcgaaaatcacggcccaaggtctggatatagttattggagac chr2 51 84460474 84460524 gccattcttgcgaaaatcacggcccaaggtctggatatagttattggagac + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_6 51 1 51 ccagcttttaatacacatatgtacatacatatgtgcataacaaattatagc chr12 51 45602556 45602606 ccagcttttaatacacatatgtacatacatatgtgcataacaaattatagc - 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_7 51 1 51 ttgagcttgaacgctttctttattggtggctgcttttaggcctacaatggt chr10 51 95540393 95540443 ttgagcttgaacgctttctttgttggtggctgcttttaggcctacaatggt + 1 mmmmmmmmmmmmmmmmmmmmmMmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_8 51 1 51 ggtgtccctgggatactcatagcctcagactggttacagagttggggcttt chr15 51 102043274 102043324 ggtgtccctgggatactcatagcctcagactggttacagagttggggcttt - 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_9 51 1 51 accattgtcgtccagagctccgtccacaccatagctccatcccttgccaca chr5 51 53673136 53673186 accattgtcgtccagagctccgtccacaccatagctccatcccttgccaca - 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_11 51 1 51 ctggagtcttggaagcttgactaccctacgttctcctacaatggaccttga chr9 51 78023154 78023204 ctggagtcttggaagcttgactaccctacgttctcctacaatggaccttga + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_12 51 1 51 tgtggggattgccctgatgctgacaaagtcagggcaggagtcagaagaaat chr15 51 8585628 8585678 tgtggggattgccctgatgctgacaaagtcagggcaggagtcagaagaaat + 0mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_13 51 1 51 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc chrX 51 66859072 66859122 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_13 51 1 51 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc chr2 51 75029531 75029581 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_2 51 1 51 ggcaagggaagaagacttcaggccactgggaaatgcttggttctgttcagt chr4 51 133526049 133526099 ggcaagggaagaagacttcaggccactgggaaatgcttggttctgttcagt + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_5 51 1 51 gccattcttgcgaaaatcacggcccaaggtctggatatagttattggagac chr2 51 84460474 84460524 gccattcttgcgaaaatcacggcccaaggtctggatatagttattggagac + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_6 51 1 51 ccagcttttaatacacatatgtacatacatatgtgcataacaaattatagc chr12 51 45602556 45602606 ccagcttttaatacacatatgtacatacatatgtgcataacaaattatagc - 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_7 51 1 51 ttgagcttgaacgctttctttattggtggctgcttttaggcctacaatggt chr10 51 95540393 95540443 ttgagcttgaacgctttctttgttggtggctgcttttaggcctacaatggt + 1 mmmmmmmmmmmmmmmmmmmmmMmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_8 51 1 51 ggtgtccctgggatactcatagcctcagactggttacagagttggggcttt chr15 51 102043274 102043324 ggtgtccctgggatactcatagcctcagactggttacagagttggggcttt - 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_9 51 1 51 accattgtcgtccagagctccgtccacaccatagctccatcccttgccaca chr5 51 53673136 53673186 accattgtcgtccagagctccgtccacaccatagctccatcccttgccaca - 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_11 51 1 51 ctggagtcttggaagcttgactaccctacgttctcctacaatggaccttga chr9 51 78023154 78023204 ctggagtcttggaagcttgactaccctacgttctcctacaatggaccttga + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_12 51 1 51 tgtggggattgccctgatgctgacaaagtcagggcaggagtcagaagaaat chr15 51 8585628 8585678 tgtggggattgccctgatgctgacaaagtcagggcaggagtcagaagaaat + 0mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_13 51 1 51 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc chrX 51 66859072 66859122 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
seq_13 51 1 51 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc chr2 51 75029531 75029581 ctttctttacaatgaccaagttgagaacactgagattagcgtccacaatgc + 0 mmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmm
Does anyone know what the issue is? Any help appreciated. Thanks!
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