Hi all, currently I'm learning how to use mirdeep2 software. Just for training purposes I'm trying to find whitefish miRs from deep sequencing data in comparison to Salmo salar genome (found here: http://www.ncbi.nlm.nih.gov/Traces/w...AGKD01#contigs). Anyway that shouldn't be a problem for mirdeep analysis.
After indexing Ssa genome by bowtie-build I used mapper.pl to process deep sequencing reeds and map them to the genome (as explained in the documentation). After that I try to use miRDeep2.pl but I'm facing some problems. First of all (as I understand) mirdeep requires single .fa file of the genome, so I merged those 4 .fa files into one:
.
Than I removed whitespaces from merged file:
.
Than I tried to run mirdeep2.pl using:
But after a while program stops and report.log contains:
Grep command shows, that it is not true:
I'm now stuck and looking forward for your help.
P.S. Just a idea from now: genome was indexed by bowtie using downloaded 4 files, not merged. It doesn't seem for me, but maybe this is part of the problem?
After indexing Ssa genome by bowtie-build I used mapper.pl to process deep sequencing reeds and map them to the genome (as explained in the documentation). After that I try to use miRDeep2.pl but I'm facing some problems. First of all (as I understand) mirdeep requires single .fa file of the genome, so I merged those 4 .fa files into one:
Code:
cat * > ssa.merged.genome.fa
Than I removed whitespaces from merged file:
Code:
sed -i 's/ /_/g' ssa.merged.genome.fa
Than I tried to run mirdeep2.pl using:
Code:
miRDeep2.pl reads_collapsed.fa ssa.merged.genome.fa reads_collapsed_vs_genome.arf mature_ref_this_species.fa mature_ref_other_species.fa precursors_ref_this_species.fa 2> report.log
Code:
#Starting miRDeep2 /home/maciek/Bin/mirdeep2/miRDeep2.pl reads_collapsed.fa ssa.merged.genome.fa reads_collapsed_vs_genome.arf mature_ref_this_species.fa mature_ref_other_species.fa precursors_ref_this_species.fa miRDeep2 started at 13:29:59 mkdir mirdeep_runs/run_11_06_2014_t_13_29_59 The mapped reference id gi|353895532|gb|AGKD01555787.1| from file reads_collapsed_vs_genome.arf is not an id of the genome file ssa.merged.genome.fa
Code:
[maciek@acer722 Salmo.salar.genome]$ grep 353895532 ssa.merged.genome.fa >gi|353895532|gb|AGKD01555787.1|_Salmo_salar_Contig_556124,_whole_genome_shotgun_sequence
P.S. Just a idea from now: genome was indexed by bowtie using downloaded 4 files, not merged. It doesn't seem for me, but maybe this is part of the problem?
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