Question about bowtie

Question

[biolab]

Dear All

I am new to use Bowtie. I need to remove rRNAs, tRNAs, snRNAs and snoRNAs from sequencing data. My approach is: (i) download Rfam db, and extract the structural RNAs of the species studied; (ii) map reads onto these structural RNAs using Bowtie, and get the list needed to discard.

After bowtie, I have a .bam file, but don't know how to get the list (the bam file is a binary file). Could you help to do me a favor? Thank you very much.

[zulk]

Dear biolab,

I also need to remove rRNAs, tRNAs, snRNAs and snoRNAs from sequencing data. I downloaded all plant noncoding rnas from NCBI. But I dont know how to use bowtie. Can you tell me step by step code. thanks in advance

[biolab]

Hi Zulfikar,

This post was 4 months ago. I suggest you use bowtie2.

First, you need to download r/t/sn/snoRNAs datasets from http://www.sanger.ac.uk/resources/databases/rfam.html, save them in a file structuralRNA.fa. Then build bowtie index for them using the command bowtie2-build structuralRNA.fa struRNA. Suppose your sequencing data is the file seqdata.fq, run bowtie to retrieve the reads unmapped on structural RNAs following the command bowtie2 -x struRNA -U seqdata.fq -S seqdata.sam --un seqdata_removerRNA.fq. Now you get the r/t/sn/snoRNA removed data, the fastq file seqdata_remove_rRNA.fq.

I should note the above are default parameters, detailed usage please see bowtie manual, I normally use default.

For further analyses, for example to convert fastq to fasta, use FastXtoolkit, to get bam file, run samtools view -bS seqdata.sam > seqdata.bam. Please read manuals and other posts for further details.

[zulk]

Thank you bio lab I am trying it with bowtie1 (not bowtie 2), because all papers do this with bowtie.

[biolab]

Thanks for your attention. I think I solved the problem, but I am really new to perform mapping. I used bowtie-build, and then bowtie -f -v 1 --best -k 1 --norc -S stru_RNA.fa reads.fa list I saw the IDs of the mapping reads on the list file.

Answer 1

[Devon Ryan]

You just need to add the --un filename option.

[biolab]

Thank you very much!

[kuttibiotech2009]

Hi,

As per your explanation, we have to take seqdata_removerRNA.fq for further analysis. Is it?

This is my command. Is this ok to process?

bowtie -q -v 1 --best -k 1 --norc -S stru_RNA.fa BH_R1.fastq BH --un seqdata_removerRNA.fastq