Question: please help with quantifier.pl error
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gravatar for A
3.2 years ago by
A3.6k
A3.6k wrote:

hi,

I was indentifying miRNAs by mirdeep2, for two fastq files I got result by for the third nothing :( :( :( how possible

I built index

bowtie-build genome.fa genome

I used mapper

[izadi@lbox200 bin]$ mapper.pl 3.fq -e -h -m -v -p af -s 3.fa -t 3.arf

parsing fastq to fasta format

discarding short reads

collapsing reads

mapping reads to genome index

trimming unmapped nts in the 3' ends

Log file for this run is in mapper_logs and called mapper.log_31816

Mapping statistics

#desc   total   mapped  unmapped    %mapped %unmapped

total: 2906658  704337  2202321 0.242   0.758

seq: 2906658    704337  2202321 0.242   0.758

but when quantifying nothing happened

quantifier.pl -p hairpin.fa -m mature.fa -r sample.fa

getting samples and corresponding read numbers

Converting input files

building bowtie index

mapping mature sequences against index

mapping read sequences against index

Mapping statistics

**No mapping file given**

how possible I got result for two samples but for third I donno what happened

any suggestion...

mirnas rna-seq mirdeep2 • 982 views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by A3.6k
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