Genome indexing
What are the different tools we can use for genome indexing?
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Marco Pannone •
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Roy.anupama11 •
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Roy.anupama11 •
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Very vague question, it depends on what you are going to do afterward.
Supposing you have a genome in .fasta format and you are going to align some sequencing data, you need to index it with the specific tool you are using for alignment.
Examples: Bowtie2; HISAT2.
Actually I came across Picard (https://github.com/broadinstitute/picard) and BWA. I wanted to re-confirm. Since I never used both. I have used HISAT2. Instead of BWA, can I use HISAT2?
What type of data do you have? RNA-seq?