bowtie2 alignment to rRNA, ERCC spike ins, Repetitive Elements and index creation

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5.0 years ago

Melonhead ▴ 10

I have downloaded .fastqfiles from SRA and now trying to filter out reads aligning to ERCC spike ins, rRNA and Repetitive Elements (from RepeatMasker).

I would like to do this step by step, repeating the command on the unaligned results from the previous step using something like this:

bowtie2 -p 2 - N1 --un-conc <unaligned fastq> --al-conc <aligned fastq> \
    -1 <dowloaded mate1 fastq. -2 <downloaded mate 2 fastq> \
    -S <output alignment sam>

As I got from the manual, first I need to build .bt2 indices for each alignment (namely, for ERCC, rRNA, RepetitiveElements) How can I create indices for the aforementioned command and which data should I download for it?

Would be happy for any help!

RNA-Seq alignment • 1.1k views

ADD COMMENT • link updated 4.8 years ago by Biostar 20 • written 5.0 years ago by Melonhead ▴ 10

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Hi artem.baranowsky, welcome.

Please use the formatting bar to highlight code. I made the changes for you this time.

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ADD REPLY • link 5.0 years ago by ATpoint 81k

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Apologies, will do next time Thank you

ADD REPLY • link 5.0 years ago by Melonhead ▴ 10

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