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Sequence Alignment using Bowtie2

Hello, I have been working on the metagenomics Illumina paired end data (2x150 seq length), but came across with a mistake done by me.

Now, I have the filtered, adapter free, high quality sequences which I need to align to the cpn60 database and remove the mapped reads so that I have the sequences which are not included in that dataset. Even after reading the manual I have a very vague idea about how to process, because the last command which I used did not help in anyways. So, if anyone can help me with command line of using the bowtie2 for removing the mapped sequences.

The command which i used last time is as follows:

download/compile: cat cpn60_ref_nut_seq.fa > cpn60.fna

bowtie2-build: bowtie2-build cpn60.fna filename

bowtie2-inspect: bowtie2-inspect cpn60(filename)

bowtie2 alignment: bowtie2 -p 8 -x cpn60 -f virus1.contigs.genes.fna -S virome.sam

genome alignment next-gen
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written by vishalchanda364 • vishalchanda364

What's the problem with the last command? (if it doesn't work, please try running it without the -p 8 option)

If the last command works and you have the samfile, you can use samtools to only get the unmapped reads,...

Please check the following links:

How To Filter Mapped Reads With Samtools

http://seqanswers.com/forums/showthread.php?t=41288&highlight=bbsplit

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

http://bowtie-bio.sourceforge.net/tutorial.shtml

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written by Fatima Fatima

Thank you so much for the help, I thought my commands had some issue with the result. Now, I got it that filtering reads is a separate step.

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written by vishalchanda364 • vishalchanda364

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