Question: Using Bowtie and SRA mode
0
gravatar for Chvatil
6 weeks ago by
Chvatil40
Chvatil40 wrote:

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 ?

Thank you for your help.

bowtie mapping • 97 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Chvatil40

Please provide full command line you are using.

ADD REPLYlink written 6 weeks ago by genomax85k

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
ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Chvatil40

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.

Download the pre-compiled binary if you can.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax85k

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...

ADD REPLYlink written 6 weeks ago by Chvatil40

Can you try with just one SRA accession?

ADD REPLYlink written 6 weeks ago by genomax85k

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

ADD REPLYlink written 6 weeks ago by Chvatil40
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