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Index file making for Triticum aestivum

Hello everybody. I want to align my rnaseq files to the reference genome of wheat using HISAT2. We need index file in it's procedure. My question is: Is there any index file for Triticum aestivum to ddownlad? Probably no. So my main question is how much memory (RAM) do I need to build that? My reference genome size is almost 17 giga base. Thank you.

rna-seq hisat index file
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updated by Laila • Laila • written by shokrabad • shokrabad

Probably difficult to predict accurately but you may need close to 100G of free RAM for the index creation.

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written by GenoMax GenoMax

@cpad112 that index can't be used with NGS alingers. That is just an indexed fasta file.

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written by GenoMax GenoMax

@ genomax : I realized later. Thanks

@ shokrabad : I was able to index using 32 gb RAM, core i7 machine using BWA. It took many hours via CLI. With bowtie it failed (didn't complete on galaxy). I downloaded the sequence from IWGSC (URGI).

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written by cpad0112 cpad0112

Thanks. I'm going to run using a server with 128gb RAM, 24 core. Then I'll report the result here soon.

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written by shokrabad • shokrabad

Hi @ Shokrabad, I am facing ow the same problem. Any advice?

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written by Laila • Laila

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