Question about bowtie
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.
1 answer
You just need to add the --un filename option.
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Devon Ryan
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Devon Ryan
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
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Thanks for your attention. I think I solved the problem, but I am really new to perform mapping. I used
bowtie-build, and thenbowtie -f -v 1 --best -k 1 --norc -S stru_RNA.fa reads.fa listI saw the IDs of the mapping reads on the list file.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
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 commandbowtie2-build structuralRNA.fa struRNA. Suppose your sequencing data is the fileseqdata.fq, run bowtie to retrieve the reads unmapped on structural RNAs following the commandbowtie2 -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.Thank you bio lab I am trying it with bowtie1 (not bowtie 2), because all papers do this with bowtie.