alignment with several packages

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2.3 years ago

Eunbi • 0

Hello,

I'm doing small RNA sequencing analysis.

I was wondering that it is okay to align same fasta file using several alignment packages

For example, after genome mapping with Bowtie or STAR, miRNA predicted by miRDeep2 and other small RNA matching with RNAcentral are aligned by Bowtie (<50nt) and Bowtie2 (>=50nt).

In same fasta file, is it possible that using different alignment package depending on size and type of small RNA?

Thank you for your kind reply in advance.

Eunbi

alignment rna-seq rna • 577 views

ADD COMMENT • link 2.3 years ago by Eunbi • 0

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In same fasta file, is it possible that using different alignment package depending on size and type of small RNA?

What do you mean by this? Are you looking to separate the reads (e.g. if they are less than 50 bp) so they can be aligned with bowtie v.1.x?

ADD REPLY • link 2.3 years ago by GenoMax 142k

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Thanks for your reply.

Yes, someone said to me to do align the less than 50bp reads with bowtie v.1 and do more than 50bp reads with bowtie v.2.

I wonder with this method, is there any error or consideration when I use multiple alignment packages?

ADD REPLY • link 2.3 years ago by Eunbi • 0

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