Question: error in mirdeep2 mapper
1
gravatar for A
4.0 years ago by
A3.9k
A3.9k wrote:

hi,

please help me with this obstacle :(

with this syntax I tried to map my reads on my indexed genome

[izadi@lbox200 bin]$ mapper.pl clean.fq -e -p Aspergillus_fumigatus -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v

but

parsing fastq to fasta format

discarding short 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_2598

Mapping statistics

desc total mapped unmapped %mapped %unmapped

Use of uninitialized value $count2 in subtraction (-) at ./mapper.pl line 708, <in> line 2451201.

Use of uninitialized value $count in subtraction (-) at ./mapper.pl line 708, <in> line 2451201.

total: Use of uninitialized value $count in print at ./mapper.pl line 708, <in> line 2451201.

Use of uninitialized value $count2 in print at ./mapper.pl line 708, <in> line 2451201.

0   Use of uninitialized value $count in division (/) at ./mapper.pl line 709, <IN> line 2451201.

Use of uninitialized value $count2 in division (/) at ./mapper.pl line 709, <in> line 2451201.

Illegal division by zero at ./mapper.pl line 709, <in> line 2451201.

[izadi@lbox200 bin]$

mirnas rna-seq mirdeep2 perl • 1.4k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by A3.9k
2
gravatar for A
4.0 years ago by
A3.9k
A3.9k wrote:

[izadi@lbox200 bin]$ mapper.pl clean.fq -e -h -m -v -p Aspergillus_fumigatus -s sample.fa -t Sample.arf

ADD COMMENTlink written 4.0 years ago by A3.9k
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