Question: bowtie2 alignment to rRNA, ERCC spike ins, Repetitive Elements and index creation
gravatar for Melonhead
10 days ago by
Melonhead0 wrote:

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 • 58 views
ADD COMMENTlink modified 8 days ago by h.mon25k • written 10 days ago by Melonhead0

Hi artem.baranowsky, welcome.

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

enter image description here

ADD REPLYlink modified 10 days ago • written 10 days ago by ATpoint16k

Apologies, will do next time Thank you

ADD REPLYlink written 10 days ago by Melonhead0
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