Using Bowtie and SRA mode
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24 months ago
Chvatil ▴ 70

Hello I need to map reads on a genome in fasta file format.

For that I installed Bowtie2 v2.4.1(last version) with biodonda by doing :

conda install bowtie2


Everything went right and I can run bowtie2 properly.

But I need to use the --sra-acc option and in the documentation they say :

As of version 2.3.5 bowtie2 now supports aligning SRA reads. Prepackaged builds will include a package that supports SRA


and unfortunatly when I use this option I get :

/beegfs/data/my_conda/bin/bowtie2-align-s: unrecognized option '--sra-acc'


So I wondered if you got the same issue when installing bowtie2 with bioconda and if you have a solution in order to add this particular option ?

bowtie mapping • 812 views
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Please provide full command line you are using.

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I built my db with :

 /beegfs/data/my_conda/bin/bowtie2-build -f /beegfs/data/Genomes/Vcanescens/Vcanescens.fa Bowtie_db_Vcanescens


then I ran :

 /beegfs/data/my_conda/bin/bowtie2 -x /beegfs/data/Genomes/Vcanescens/Bowtie_db_Vcanescens -S /beegfs/data/Genomes/Vcanescens/Mapping/Bowtie_Mapping.sam --no-unal --sra-acc SRR8354698,SRR8354699,SRR8354700,SRR8354701

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I think your copy of bowtie2 has not been compiled with sra support, if you or someone compiled it locally.

As of version 2.3.5 bowtie2 now supports aligning SRA reads. Prepackaged builds will include a package that supports SRA. If you’re building bowtie2 from source please make sure that the Java runtime is available on your system. You can then proceed with the build by running make sra-deps && make USE_SRA=1.

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I tried to dowload wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1/bowtie2-2.4.1-linux-x86_64.zip but I still get the same issue it does not recognise the '--sra-acc' option...

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Can you try with just one SRA accession?

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It is the same, this is the option that is not recognized