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Question: Alignment to ref genome
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gravatar for amy16
2.1 years ago by
amy16 • 40
amy16 • 40 wrote:

I have generated the genome index using default options in HISAT2. now for the alignment purpose which if the output index files should i specify ?
rna-seq alignment • 789 views
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modified 2.1 years ago • written 2.1 years ago by amy16 • 40

What does the option wrapper means in hisat2?

ADD REPLY • link written 2.1 years ago by amy16 • 40
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gravatar for biplab
2.1 years ago by
biplab • 100
University of California, Davis
biplab • 100 wrote:

You just need to specify the basename (part of the filename common to all of your index files) of index files. For example using genome.fa file as input in hisat2-buil we get these files as output(genome.1.ht2 genome.2.ht2 genome.3.ht2 genome.4.ht2 genome.5.ht2 genome.6.ht2 genome.7.ht2 genome.8.ht2). You just need to specify path to the index directory and basename(genome).
ADD COMMENT • link written 2.1 years ago by biplab • 100

Thank you for the reply. Will try it now

ADD REPLY • link written 2.1 years ago by amy16 • 40

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLY • link written 2.1 years ago by WouterDeCoster ♦ 42k
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