Alignment to ref genome
1 answer
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).
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
• 0 views
•
link
written
by
WouterDeCoster
Log in to answer this question.
More posts like this
-
Hisat2 index and alignment question
written by Athena •
-
HISAT2_linux
written by Pegasus •
-
RNA-Seq read alignment genomic and transcriptomic
written by imaparna27 •
-
Infer experiment - Failed to determine strandin paired end stranded RNA-seq
written by GiusiG •
-
Sam file manipulation
written by abhijit.synl
-
Picking the right genome annotation for RNA-seq
written by Thomas •
-
Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis
written by amy16 •
-
RNA-seq read alignment
written by amy16 •
-
Alignment parameters within Hisat2
written by amy16 •
-
Reference genome alignment
written by amy16 •
What does the option wrapper means in hisat2?