Ok. I shall check it. Thank you so much.
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mirDeep2 mapping error
Hi all,
Kindly help me with this issue
shanthi@shanthi-client2:~/Desktop/Nivya/Fastq files/SRR7189567-stage 1A$ mapper.pl trim_3_SRR7189567.fastq -e -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -p genome -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v -n -h
parsing fastq to fasta format
discarding sequences with non-canonical letters
clipping 3' adapters
discarding short reads
collapsing reads
mapping reads to genome index
Could not locate a Bowtie index corresponding to basename "genome"
Please make sure you used bowtie version 1 to build the index.
Usual index files have suffix .ebwt
I have used bowtie version 1. But i dont know why this is occuring.
Thank You in advance
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1 answer
Is the genome index directory in your current path (~/) ? Otherwise you should had the absolut path of the genome index directory in your command line.
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Bastien Hervé
Thank You so much Bastein i was able to get the results when done like you suggested.
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Please add the command you used to generate the genome index with bowtie 1
i used the command to generate bowtie files
Do you have a directory called genome with .ebwt files inside ?
Could you copy paste the log file of the bowtie-build command please
yes i do have genome directory with .ebwt files.. but there are no log files other than .ebwt files inside. but after doing the mapper.pl function there is a bowtie log file. Kindly check these files
Please make sure the index name which you have provided during bowtie-build is same as what you are providing after '-p' option.
Yes. i checked again. It is the same index name that i have provided after -p option.