Question: Alignment to ref genome
0
gravatar for amy16
2.1 years ago by
amy1640
amy1640 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
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by amy1640

What does the option wrapper means in hisat2?

ADD REPLYlink written 2.1 years ago by amy1640
2
gravatar for biplab
2.1 years ago by
biplab100
University of California, Davis
biplab100 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 COMMENTlink written 2.1 years ago by biplab100

Thank you for the reply. Will try it now

ADD REPLYlink written 2.1 years ago by amy1640

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 REPLYlink written 2.1 years ago by WouterDeCoster42k
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