help to hisat2-build index command
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4 days ago
Hien • 0

I have got the question about RNA-seq as below:

To generate the genome index for Hisat2 we will need a FASTA file representing the genome of interest. During this exercise, we will use the sequence of the human genome GRCh38.p13 (Genome Reference Consortium Human Build 38 patch release 13). Given the genome size and the scope of this exercise, running an alignment against the entire genome would take too long, so we will work on a single chromosome, chromosome X. You will find the sequence of this chromosome in references/fasta/GRCh38.p13.chrX.fa. Task: Generate the index files (hint: hisat2-build). Make your index aware of splicing junctions, exons, haplotype, and SNPs. Use the files references/gencode.v32.exons.tsv, references/gencode.v32.ss.tsv, references/snp144Common.haplotype, and references/snp144Common.snp. Save the results in the hisat2/index folder. Could any one explain what exactly I must do? I did not fully understand the mean of task. Thank you so much!

sequencing hisat2 index RNA • 78 views
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Since this is an assignment which you bluntly copied I suggest you read the hisat manual and figure it out on your own. Same goes for subsetting a fasta based on chromosomes. Use google and our search functions, plenty of threads on that available.

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